DIAGNOSTIC, PROGNOSTIC AND THERAPEUTIC USES OF LONG NONCODING RNAs FOR PATHOLOGIES AND TOXICITIES INDUCING HEART DISORDERS

ABSTRACT

The present invention provides methods for the diagnosing, monitoring and prognostication of primary and secondary cardiac disorders in a subject based on lncRNA expression. The invention also provides methods for predicting heart failure after myocardial infarction, and differenciation of Ischemic versus non-ischemic Heart Failure. The assessment/quantification of these lncRNAs may also be used as a marker for monitoring drug-induced cardiac toxicities and for the assessment of cardiac involvement during systemic diseases and others disorders/toxicities impacting cardiac function. These lncRNAs are cardiac tissue enriched and may be involved in different cardiac pathophysiological events and represent a potential target for therapeutical approaches.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit and priority of U.S. provisional application 62/518,418, filed on Jun. 12, 2017.

The present invention provides new biomarkers and methods for the diagnosing, monitoring and prognostication of primary and secondary cardiac disorders in a subject based on lncRNA expression. The invention also provides methods for predicting heart failure (HF) after myocardial infarction, or differentiation between Ischemic (ICM) versus non-ischemic (Non-ICM) HF (e.g., dilated cardiomyopathy (DCM)). The assessment/quantification of these lncRNAs in a single mode or in combination with other lncRNAs can also be used as a marker for monitoring drug-induced cardiac toxicities and for the assessment of cardiac involvement during systemic diseases and others disorders/toxicities impacting cardiac function. These lncRNAs are cardiac tissue enriched and may be involved in different pathophysiological events pertaining to cardiac function and represent a potential target for therapeutic approaches. These therapeutic approaches may be inhibitors or activators of these lncRNAs or the products activated or inhibited by these lncRNAs.

FIELD OF THE INVENTION

The present invention provides a list of cardiac associated or cardiac-enriched lncRNAs and methods for monitoring and diagnosing cardiac disorders in a subject based on lncRNA expression. The invention also provides methods for diagnosing different types of HF such as ICM versus Non-ICM (e.g., DCM), methods for predicting HF after myocardial infarction, and for monitoring treatment efficacy and drug-induced cardiac toxicities.

BACKGROUND OF THE INVENTION

In recent years, long non-coding RNA (lncRNAs) have emerged as a new type of non-coding RNA and many studies have shown their potential as powerful biomarkers in various pathologies such as cancer.

In contrast to other non-coding RNA such as miRNA or snoRNA, lncRNA lack strong whole sequence conservation across different species but rather appear to contain short, highly conserved elements. Despite only a few lncRNA having been shown to be biologically relevant and functionally annotated, there's growing evidence that the majority of them are likely to be functional. While the exact function of most lncRNAs remain unknown, they have been implicated in various biological processes, mainly relating to transcriptional, post-transcriptional and epigenetic regulation. The majority of lncRNAs to date, that are functionally characterized, are believed to regulate developmental processes. However, recent profiling of the mice cardiac transcriptome, after myocardial infarction in mice cardiac tissue, has shown their role in controlling mature tissue as well as the relevance of their expression level in cardiac pathologies. There are publications which have argued for apparent similar roles of certain lncRNAs in humans e.g., WO2015092020,

Cardiac disorders such as coronary artery disease (CAD), acute myocardial infarcation (AMI) and heart failure (HF) are leading causes of mortality and morbidity in the world and cardiac toxicities such as those induced by drugs and drug candidates are the most important cause of drug withdrawal. Thus, there is a very important unmet medical need for diverse types of biomarkers for assessing cardiac function, including but not limited to diagnosis, prognosis, monitoring of drug effects and diseases activity. Several cardiac pathologies remain still incurable or need less aggressive and more personalized treatment. lncRNA represent a novel family of targets useful for these diagnostic and therapeutic applications in the cardiovascular area. The present invention relates to lncRNAs that are cardiac enriched and described for the first time in human cardiac tissues. They represent good therapeutic and diagnostic candidates for cardiac related disorders.

SUMMARY OF THE INVENTION

Given that expression levels of lncRNAs could be associated with heart disease in human cardiac biopsies, the inventors set out to characterize lncRNA specifically relevant to cardiac tissue and involved in cardiac remodeling.

The present invention relates to lncRNAs having a sequence selected from the group consisting of SEQ ID NO 1 to SEQ ID NO 3238 (Human sequences) isoforms thereof, fragments thereof and variant sharing at least 80% nucleotide sequence homology (hereinafter named “lncRNA of the invention”) suitable for the diagnosis, prognosis and monitoring of subjects suffering from cardiovascular disorders.

In particular, the invention provides a method for diagnosing and monitoring cardiac disorders, the method comprising determining the level of expression, in a biological sample derived from said subject, of one or more lncRNAs of the invention and calculating differential expression of one of more lncRNAs of the invention compared to one or more lncRNA in a biological sample from a control subject, wherein differential expression of one or more lncRNAs of the invention indicates that the subject has developed or is at risk of developing a cardiac disorder. This method of the invention is also suitable for the prognostication of cardiac disorders.

In another aspect, the invention provides a method for predicting the development of heart failure (HF) in a subject having suffered myocardial infarction, a method for monitoring treatment efficacy in a subject suffering from cardiac injury and receiving a pharmaceutical cardiac therapy, a method for evaluating drug-induced cardiac toxicity in a subject receiving an effective amount of pharmaceutical composition, a method for diagnosing ischemic cardiomyopathy (ICM) in a subject, a method for diagnosing dilated cardiomyopathy (DCM) in a subject, a method for differentiating ICM vs Non-ICM (e.g., DCM) in subjects suffering heart failure, the methods comprising determining the level of expression, in a biological sample derived from said subject, of one or more lncRNAs of the invention and calculating differential expression of one of more lncRNAs of the invention compared to one or more lncRNA in a biological sample from a control subject.

In another aspect, the invention concerns a diagnostic/prognostic kit for carrying out any of the before cited methods.

In still another aspect, the present invention provides a method for treating a cardiac pathology in a subject comprising administering to said subject an effective amount of a pharmaceutical agent modulating the expression of one or more lncRNAs of the invention.

It yet another aspect, the invention provides for a method of detecting one or more lncRNAs (e.g., lncRNAs having a sequence selected from the group consisting of SEQ ID NO 1 to SEQ ID NO 3238). In one aspect, the method comprises the step of obtaining the lncRNA from a human biological sample (e.g., a human plasma sample).

In still another aspect, the invention provides a method of obtaining one or more lncRNAs, wherein the method comprises selection and isolation of total RNA. In one aspect, the lncRNA is correlated with the risk or development of a cardiac disorder. In one aspect the lncRNA is obtained from a biological sample (e.g., a cardiac biopsy or blood sample (e.g., plasma sample)).

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows the sequencing data analysis and the selection procedure of known lncRNA relevant to the cardiac pathologies.

FIG. 2 shows the sequencing data analysis and the selection procedure of novel identified lncRNA relevant to the cardiac pathologies.

FIGS. 3A and 3B show the correlation between results obtained by sequencing with both Cuffdiff (middle bar) and DeSeq (right bar) analysis and results obtained by PCR (left bar) on patients of the same conditions. FIG. 3A compares ICM and Control. FIG. 3B compares DCM and Control.

FIG. 4 shows the expression of 4 lncRNA in human plasma samples as analyzed by qRT-PCR after preamplification: AMI indicated by a square and Control indicated by a circle.

FIG. 5 shows a histogram with the number of lncRNA, which passed the different threshold of coverage depth (in horizontal axis). In total RNA-seq protocol (left bar), half of 3238 lncRNA have an average coverage depth less than 2×. In FiMICS (targeted sequencing) protocol (right bar), more than 3000 lncRNA have at least an average coverage depth of 2×.

FIG. 6 shows Venn diagram of the significantly expressed lncRNAs from analysis of RNASeq and FiMICS data generated in serum samples collected at D3 of patients with AMI for the prediction of ventricular remodeling measured by the Echocardiography at month 1 post PCI. Low LVEF corresponding to the ventricular remodeling is grouped using two thresholds: either LVEF<40% or 45%.

DETAILED DESCRIPTION OF THE INVENTION

The Inventors intended to characterize the cardiac long non-coding transcriptome and more particularly the dynamically modulated fraction after left ventricular remodeling. The Inventors performed deep RNA-sequencing of cardiac biopsies coupled to novel transcript reconstruction and integration in genome-wide data sets as well as previously characterized predicted human cardiac-specific lncRNA to systematically identify and annotate heart-specific lncRNAs.

Surprisingly, it has been found that the lncRNAs of the invention are highly cardiac and context specific, thus providing a high potential as biomarkers of cardiac disorders as well as pathological response and physiological homeostasis. In addition, using novel transcripts reconstruction, novel lncRNA never described before that are cardiac-enriched and differentially expressed in cardiomyopathies have been found. These findings have been validated by comparing their RNA-Seq data with qPCR data from patients suffering the same conditions. A number of these human lncRNAs are detected in human plasma samples, supporting the feasibility of measuring their expression in patient biofluids for diagnosis and prognosis purposes. Furthermore, the inventors have identified lncRNAs which are differentially expressed in blood sample between the low LVEF (left ventricular ejection fraction) group and the high LVEF group after PCI (Percutaneous Coronary Intervention). Collectively, a novel panel of heart-specific lncRNAs with unique prognosis value relevant to cardiac disorders has been found.

As used herein, a control sample refers to a biological sample such as tissue or cells (e.g., blood sample) from a normal subject (e.g. an individual who does not have cardiac disease or any condition or symptom associated with).

As used herein, “identity” refers to the sequence matching between two polypeptides, molecules or between two nucleic acids. When a position in both of the two compared sequences is occupied by the same base or amino acid monomer subunit (for instance, if a position in each of the two DNA molecules is occupied by adenine, or a position in each of two polypeptides is occupied by a lysine), then the respective molecules are identical at that position. The “percentage identity” between two sequences is a function of the number of matching positions shared by the two sequences divided by the number of positions compared times 100. Such alignment can be provided using, for instance, the program Basic Local Alignment Search Tool (BLAST) from the National Center for Biotechnology Information NCBI.

The one or more lncRNAs, fragments thereof, isoforms thereof and variants sharing at least 80% nucleotide sequence identity thereto listed in Table 1 are not part of the present invention. The sequences of these one or more lncRNAs, excluded from the present invention, are described in PCT/EP2014/078868 (Université de Lausanne) and in filed in ST25 format.

TABLE 1 XLOC_ID Physiology Cluster Lnc XLOC_007900 1 Lnc7900 XLOC_008052 1 Lnc8052 XLOC_006224 1 Lnc6224 XLOC_013471 1 Lnc13471 XLOC_002075 1 Lnc2075 XLOC_023749 1 Lnc23749 XLOC_008063 1 Lnc8063 XLOC_024203 1 Lnc24203 XLOC_019889 1 Lnc19889 XLOC_008229 1 Lnc8229 XLOC_014116 1 Lnc14116/Novlnc11 XLOC_003166 1 Lnc3166 XLOC_010335 1 Lnc10335 XLOC_021863 1 Lnc21863 XLOC_012367 1 Lnc12367 XLOC_007833 1 Lnc7833 XLOC_023850 2 Lnc23850 XLOC_029624 2 Lnc-TEAD1 XLOC_022865 2 Lnc-SE-22865 XLOC_018239 2 Lnc18239 XLOC_022715 2 Lnc-COL16A1 XLOC_013413 2 Lnc13413 XLOC_005390 2 Lnc-MEOX1 XLOC_010961 2 Lnc-WISP1 XLOC_000709 2 Lnc-TGFB2 XLOC_013407 2 Lnc-SLC8A1 XLOC_020214 2 Lnc-CYR61 XLOC_012723 2 Lnc-SE-12723/Novlnc174 XLOC_022262 2 Lnc22262 XLOC_000719 2 Lnc00719 XLOC_004951 2 Lnc4951 XLOC_026589 2 Lnc26589 XLOC_019010 2 Lnc19010 XLOC_022236 2 Lnc22236 XLOC_011236 3 Lnc-SLC38A2 XLOC_012015 3 Lnc-KCNJ6 XLOC_012884 3 Lnc-NKX2.5 XLOC_004797 3 Lnc4797 XLOC_003851 3 Lnc-SPNB2 XLOC_011237 3 Lnc-SLC38A2 XLOC_014898 3 Lnc-SE-14989 XLOC_030839 3 Lnc-CDH13 XLOC_012194 3 Lnc-ACAP2 XLOC_031308 3 Lnc-IRX3 XLOC_026621 3 Lnc-ATOH8 XLOC_002721 3 Lnc-TXLNB XLOC_003170 3 Lnc-KITLG XLOC_002849 4 Lnc-Novlnc6 XLOC_016279 4 Lnc-Novlnc25 XLOC_024141 4 Lnc-CARD11 XLOC_021524 4 Lnc-NFIB XLOC_021715 4 Lnc-FOXO6 XLOC_020321 4 Lnc-ANX5A XLOC_006274 4 Lnc-MAX XLOC_021416 4 Lnc21416 XLOC_003767 4 Lnc-LIF XLOC_014118 4 Lnc-LCLAT1 XLOC_004833 4 Lnc4833 XLOC_009582 4 Lnc-PPIF XLOC_024449 4 Lnc24449 XLOC_006146 4 Lnc6146 XLOC_033521 4 Lnc-Dedbt (Lnc033521) XLOC_025643 4 Lnc25643 XLOC_004910 4 Lnc-SPARC XLOC_010967 4 Lnc-miR30b XLOC_002503 4 Lnc-SOCS2 XLOC_017764 4 Lnc-ID1 XLOC_020119 4 Lnc20119 XLOC_001065 4 Lnc-GPC1 XLOC_009131 4 Lnc-OTX2 XLOC_000264 4 Lnc-FAM124B XLOC_032325 4 Lnc-TALIN1 XLOC_002546 4 Lnc-KRR1 XLOC_006241 4 Lnc-DACT1 XLOC_029781 4 Lnc29781 XLOC_030722 4 Lnc-SE-30722 XLOC_032031 4 Lnc-KCNJ XLOC_020634 4 Lnc-SE-20634 XLOC_031524 4 Lnc-IRF2BP2 XLOC_020212 4 Lnc-CYR61 XLOC_000336 4 Lnc-HDAC4 XLOC_015960 4 Lnc-ITPRIP XLOC_004067 4 Lnc-MYOCD XLOC_015277 4 Lnc-SMAD7/Novlnc23 XLOC_020313 4 Lnc20313 XLOC_008190 4 Lnc8190 XLOC_033125 4 Lnc33125 XLOC_032788 4 Lnc32788/Novlnc90 XLOC_014917 4 Lnc14917 XLOC_014935 4 Lnc14935 XLOC_007419 4 Lnc7419 XLOC_006561 4 Lnc6561 XLOC_024370 4 Lnc24370 XLOC_006255 4 Lnc6255 XLOC_029637 4 Lnc29637 XLOC_010855 2 Lnc10855 XLOC_007852 4 Lnc7852/Novlnc15 XLOC_009335 4 Lnc9335/Novlnc32 XLOC_019782 2 Lnc19782/Novlnc35 XLOC_010735 4 Lnc10735/Novlnc44 XLOC_007917 4 Lnc7917/Novlnc61 XLOC_033357 4 Lnc33357 XLOC_023848 4 Lnc23848/Novlnc49 XLOC_016979 4 Lnc16979

The present invention relates to lncRNAs having a sequence selected from the group consisting of SEQ ID NO 1 to SEQ ID NO 3238 (Human sequences) isoforms thereof, fragments thereof and variant sharing at least 80% (e.g., at least 90%, at least 95%, at least 98%, or at least 99%) nucleotide sequence homology suitable for the diagnosis, prognosis and monitoring of subjects suffering from cardiovascular disorders.

In some embodiments, the lncRNA which is detected is selected from any of SEQ ID NO: 1-SEQ ID NO: 3238.

In some embodiments, the lncRNA which is detected is selected from the group consisting of:

-   -   (i) 15 lncRNAs of SEQ ID 1204, SEQ ID 1736, SEQ ID 0544, SEQ ID         0915, SEQ ID2368, SEQ ID 1595, SEQ ID 2382, SEQ ID 0859, SEQ ID         3112, SEQ ID 1869, SEQ ID 1406, SEQ ID 0043, SEQ ID 0363, SEQ ID         0069 and SEQ ID 1947;     -   (ii) 11 lncRNAs of SEQ ID 2373, SEQ ID 1748, SEQ ID 3112, SEQ ID         1231, SEQ ID 0664, SEQ ID 1686, SEQ ID 0791, SEQ ID 2126, SEQ ID         2750, SEQ ID 3010, and SEQ ID 2241;     -   (iii) 14 lncRNAs of SEQ ID 2150, SEQ ID 1534, SEQ ID 0311, SEQ         ID 2952, SEQ ID 2838, SEQ ID 1437, SEQ ID 1297, SEQ ID 1059, SEQ         ID 1465, SEQ ID 2826, SEQ ID 0180, SEQ ID 0538, SEQ ID 0258, and         SEQ ID 2273;     -   (iv) 20 lncRNAs of SEQ ID 0190, SEQ ID 0359, SEQ ID 0776, SEQ ID         1421, SEQ ID 1795, SEQ ID 0477, SEQ ID 1511, SEQ ID 0435, SEQ ID         1418, SEQ ID 1025, SEQ ID 0265, SEQ ID 1311, SEQ ID 2540, SEQ ID         2323, SEQ ID 3011, SEQ ID 2447, SEQ ID 2863, SEQ ID 2697, SEQ ID         3128, and SEQ ID 2265;     -   (v) 11 lncRNAs of SEQ ID 2540, SEQ ID 0545, SEQ ID 1766, SEQ ID         3011, SEQ ID 0968, SEQ ID 2371, SEQ ID 1533, SEQ ID 0749, SEQ ID         0609, SEQ ID 1446, and SEQ ID 2986;     -   (vi) 8 lncRNAs of SEQ1204, SEQ2454, SEQ0334, SEQ1403, SEQ1089,         SEQ2692, SEQ2273, SEQ0502;     -   (vii) 4 lncRNAs of SEQ0097, SEQ1947, SEQ1051 and SEQ2996; and     -   (viii) lncRNAs in Table 4, Table 5, Table 8, Table 9, Table 12,         Table 15, Table 18, Table 19, Table 20, Table 21, Table 22,         Table 24, Table 25, Table 28, Table 29, Table 32, Table 33,         Table 34, Table 35, Table 36, Table 37, Table 38, Table 39,         Table 40, and/or Table 41.

As used herein, a biological sample may be any sample that may be taken from a subject, such as whole blood, serum, plasma, semen, saliva, tears, urine, fecal material, sweat, buccal smears, skin, cardiac tissue, liver, brain tissue, amniotic fluid, nerve tissue and hair. It also includes specific cellular subtypes or derivatives extracted from those such as PBMCs. The sample used in this invention is preferably blood or cardia tissue, more preferably blood, e.g., serum.

The expression level of lncRNAs may be determined by any technology known by a man skilled in the art. In particular, the expression level of lncRNAs is determined by measuring the amount of nucleic acid transcripts of each lncRNA. The amount of nucleic acid transcripts can be measured by any technology known by a man skilled in the art. The measure may be carried out directly on an extracted RNA sample or on retrotranscribed complementary DNA (cDNA) prepared from extracted RNA by technologies well-known in the art. From the RNA or cDNA sample, the amount of nucleic acid transcripts may be measured using any technology known by a man skilled in the art, including nucleic acid microarrays, quantitative PCR, sequencing (e.g., next generation sequencing), and hybridization with a labeled probe.

In some embodiments, the expression level of lncRNAs is determined using sequencing, e.g., next generation sequencing. Sequencing may be carried out after converting extracted RNA to cDNA using reverse transcriptase or RNA molecules may be directly sequenced. In a particular embodiment, which should not be considered as limiting the scope of the invention, the measurement of the expression level using next generation sequencing may be performed as follows. Briefly, RNA is extracted from a sample (e.g., blood sample). After removing rRNA, RNA samples are then reverse transcribed into cDNA. To ensure strand specificity, single stranded cDNA is first synthetized using Super-Script II reverse transcriptase and random primers in the presence of Actinomycin D, and then converted to double stranded cDNA with the second strand marking mix that incorporates dUTP in place of dTTP. Resulting blunt ended cDNA are purified using AMPure XP magnetic beads. After a 3′end adenylation step, adaptor is attached to cDNA. So obtained cDNA (sequencing library) may be amplified by PCR. The sequencing libraries can be sequenced by any next generation sequencing technology known by a man skilled in the art.

In some embodiments, the measurement of the expression level of lncRNAs, e.g., by sequencing (e.g., next generation sequencing), is facilitated by capturing and enriching nucleic acids (RNA or cDNA) corresponding to lncRNAs of interest prior to the measurement. As used herein, enrichment refers to increasing the percentage of the nucleic acids of interest in the sample relative to the initial sample by selectively purifying the nucleic acids of interest. The enrichment of nucleic acids corresponding to lncRNAs of interest can be carried out on extracted RNA sample or cDNA sample prepared from extracted RNA. In some embodiments, nucleic acids corresponding to lncRNAs of interest are captured and enriched by hybridizing RNA or cDNA sample to oligonucleotide probes specific to lncRNAs of interest (e.g. oligonucleotide probes comprising a sequence complementary to a region of lncRNAs of interest) under conditions allowing for hybridization of the probes and target nucleic acids to form probe-target nucleic acid complexes. Probes may be DNA or RNA, preferably DNA. The length of probes may be from 30 to 80 nucleotides, e.g., from 40 to 70, from 40 to 60, or about 50 nucleotides. The probe-target nucleic acid complexes can be purified by any technology known by a man skilled in the art. In a preferred embodiment, probes are biotinylated. The biotinylated probe-target nucleic acid complexes can be purified by using a streptavidin-coated substrate, e.g, a streptavidin-coated magnetic particle, e.g., T1 streptavidin coated magnetic bead.

In some embodiments, the expression level of lncRNAs may be determined using quantitative PCR. Quantitative, or real-time, PCR is a well known and easily available technology for those skilled in the art and does not need a precise description. In a particular embodiment, which should not be considered as limiting the scope of the invention, the determination of the expression profile using quantitative PCR may be performed as follows. Briefly, the real-time PCR reactions are carried out using the TaqMan Universal PCR Master Mix (Applied Biosystems). 6 μl cDNA is added to a 9 μl PCR mixture containing 7.5 μl TaqMan Universal PCR Master Mix, 0.75 μl of a 20× mixture of probe and primers and 0.75 μl water. The reaction consisted of one initiating step of 2 min at 50 deg. C, followed by 10 min at 95 deg. C, and 40 cycles of amplification including 15 sec at 95 deg. C and 1 min at 60 deg. C. The reaction and data acquisition can be performed using the ABI 7900HT Fast Real-Time PCR System (Applied Bio systems). The number of template transcript molecules in a sample is determined by recording the amplification cycle in the exponential phase (cycle threshold or C_(Q) or C_(T)), at which time the fluorescence signal can be detected above background fluorescence. Thus, the starting number of template transcript molecules is inversely related to C_(T).

In some embodiments, the expression level of lncRNAs may be determined by the use of a nucleic acid microarray. A nucleic acid microarray consists of different nucleic acid probes that are attached to a substrate, which can be a microchip, a glass slide or a microsphere-sized bead. A microchip may be constituted of polymers, plastics, resins, polysaccharides, silica or silica-based materials, carbon, metals, inorganic glasses, or nitrocellulose. Probes can be nucleic acids such as cDNAs (“cDNA microarray”) or oligonucleotides (“oligonucleotide microarray”), and the oligonucleotides may be about 25 to about 60 base pairs or less in length. To determine the expression profile of a target nucleic acid sample, said sample is labelled, contacted with the microarray in hybridization conditions, leading to the formation of complexes between target nucleic acids that are complementary to probe sequences attached to the microarray surface. The presence of labelled hybridized complexes is then detected. Many variants of the microarray hybridization technology are available to the man skilled in the art.

The present invention provides Method 1. Method 1 is a method of diagnosing or monitoring or treating cardiac diseases or disorders in a subject, the method comprising

-   -   a.) obtaining a sample from said subject;     -   b.) detecting the level of expression of one or more lncRNAs         (e.g., having a sequence consisting of SEQ ID NO1 to SEQ ID NO         3238, isoforms thereof, fragment thereof and variant sharing at         least 80% nucleotide sequence homology); and     -   c.) diagnosing the subject with one or mores cardiac diseases or         disorders based upon the level of expression of one or more         lncRNAs compared to a control,     -   with the proviso that the one or more lncRNAs, fragments         thereof, isoforms thereof and variants sharing at least 80%         nucleotide sequence identity thereto listed in Table 1 are not         part of the present invention.

In various aspects, Method 1 includes the following:

-   -   1.1 Method 1, wherein the method wherein the level of expression         or the differential expression of one or more said lncRNAs         indicates that the subject has developed or is at risk of         developing a cardiac disorder.     -   1.2 Method 1 or 1.1, wherein cardiac disorder is selected from         the group consisting of: pathologies or abnormalities with         Interventricular Septal Thickness (IVS), heart failure (e.g.,         left and right ventricle dilatation/dysfunction), EF, LVID, MI,         HFrEF, myocardial infarction, myocarditis (e.g., viral         myocarditis), cardiac toxicity, brachycardia, arrhythmia,         congenital heart defects, hypertension, diabetic cardiomyopathy,         idiopathic and dilated cardiomyopathy, pathologies characterized         by malformation, pathologies characterized by tissue remodeling,         pathologies characterized by affected function, pathologies         characterized by disorders of the right heart, pathologies         characterized by arrhythmias, pathologies characterized by         intoxication, pathologies characterized by cancer, pathologies         characterized by neurologic disorders, pathologies characterized         by trauma, pathologies characterized by a change in hemodynamic,         pathologies characterized by vascular disorders altering cardiac         functions such as Coronary artery disease (CAD), and pathologies         resulted from cardiac dysfunction/disorders inducing ischemic         (embolic/thrombotic) stroke.     -   1.3 The method of Method 1, 1.1, or 1.2, wherein the diagnosis         step includes predicting the development of heart failure in a         subject having suffered AMI, the method comprising determining         the level of expression, in a biological sample derived from         said subject, of one or more lncRNAs of the invention or         calculating differential expression of one of more lncRNAs         compared to one or more lncRNAs in the same biological sample,         wherein the level of expression or the differential expression         of one or more said lncRNAs predicts the risk for the subject to         develop HF.     -   1.4 The method of any of Method 1-1.3, wherein the method         optionally further comprises the step of administering at least         one pharmaceutical to the subject in order to treat one or more         cardiovascular diseases or disorders.     -   1.5 The method of any of Method 1-1.4, wherein the level of         expression refers to the differential expression of lncRNAs, the         presence of lncRNAs, or the absence of lncRNAs.     -   1.6 The method of any of Methods 1-1.5, wherein the level of         expression of one or more said lncRNAs indicates that the         subject suffers ICM.     -   1.7 The method of any of Methods 1-1.5, wherein the level of         expression of one or more said lncRNAs indicates that the         subject suffers Non-ICM (e.g., DCM).     -   1.8 The method of any of the preceding methods, wherein the         subject has been previously diagnosed with Heart Failure (e.g.,         congestive heart failure)     -   1.9 The method of 1.8, wherein the level of expression of one or         more said lncRNAs indicates that the subject with Heart Failure         also suffers Non-ICM (e.g., DCM).     -   1.10 Any of the preceding methods, wherein the biological sample         is selected from the group consisting of: whole blood, serum,         plasma, semen, saliva, tears, urine, fecal material, sweat,         buccal smears, skin, cardiac tissue, liver, brain tissue,         amniotic fluid, nerve tissue and hair (e.g, wherein the sample         is preferably plasma or cardiac tissue).     -   1.11 Any of the preceding methods, wherein the lncRNA expression         levels are detected in a sample (e.g., biological sample) using         a technique selected from the group consisting of: S1 nuclease         protection assay, microarray analysis, polymerase chain reaction         (PCR), hybridization technologies, reverse transcriptase         polymerase chain reaction (RT-PCR), Northern blot, serial         analysis of gene expression (SAGE), immunoassay, and mass         spectrometry.     -   1.12 Any of the preceding methods, wherein the lncRNA expression         level of lncRNA in sample (e.g., biological sample) is detected         using a singleplexed or multiplexed method selected from a group         consisting of: fluorescence, luminescence, radio-marking,         sequencing, e.g., next generation sequencing, and coded         microdisks.     -   1.13 Any of the preceding methods further comprising         administering a pharmaceutical composition which modulates one         or more lncRNAs, wherein the pharmaceutical composition is         selected from the group consisting of: a chemical agent, a RNA         mimic, an antibody, an engineered protease, a CRISPR based         technology and enzymatically active RNA.     -   1.14 The method of 1.13, wherein the enzymatically active RNA is         selected from the group consisting of: a miRNA, a siRNA, a         piRNA, a hnRNA, a snRNA, esiRNA, shRNA, decoys, RNA aptamers and         an antisense oligonucleotide.     -   1.15 Any of the preceding methods, wherein the method is a         method of diagnosis.     -   1.16 Any of the preceding methods, wherein the method is a         method of monitoring.     -   1.17 Any of the preceding methods, wherein the method is a         method of treatment.     -   1.18 Any of the preceding methods, wherein the expression level         of the lncRNAs of the invention are detected by measuring the         levels of cDNAs, amplified RNAs or DNAs or quantities of DNA         probes, or other molecules, in a sample (e.g., biological         sample) that are indicative of the expression level of the         lncRNA.     -   1.19 Any of the preceding methods, wherein the lncRNA which is         detected is selected from any of SEQ ID NO: 1-SEQ ID NO: 3238.     -   1.20 Any of the preceding methods, wherein the lncRNA which is         detected is selected from selected from the group consisting of:         -   (i) 15 lncRNAs of SEQ ID 1204, SEQ ID 1736, SEQ ID 0544, SEQ             ID 0915, SEQ ID2368, SEQ ID 1595, SEQ ID 2382, SEQ ID 0859,             SEQ ID 3112, SEQ ID 1869, SEQ ID 1406, SEQ ID 0043, SEQ ID             0363, SEQ ID 0069 and SEQ ID 1947;     -   (ii) 11 lncRNAs of SEQ ID 2373, SEQ ID 1748, SEQ ID 3112, SEQ ID         1231, SEQ ID 0664, SEQ ID 1686, SEQ ID 0791, SEQ ID 2126, SEQ ID         2750, SEQ ID 3010, and SEQ ID 2241;         -   (iii) 14 lncRNAs of SEQ ID 2150, SEQ ID 1534, SEQ ID 0311,             SEQ ID 2952, SEQ ID 2838, SEQ ID 1437, SEQ ID 1297, SEQ ID             1059, SEQ ID 1465, SEQ ID 2826, SEQ ID 0180, SEQ ID 0538,             SEQ ID 0258, and SEQ ID 2273;         -   (iv) 20 lncRNAs of SEQ ID 0190, SEQ ID 0359, SEQ ID 0776,             SEQ ID 1421, SEQ ID 1795, SEQ ID 0477, SEQ ID 1511, SEQ ID             0435, SEQ ID 1418, SEQ ID 1025, SEQ ID 0265, SEQ ID 1311,             SEQ ID 2540, SEQ ID 2323, SEQ ID 3011, SEQ ID 2447, SEQ ID             2863, SEQ ID 2697, SEQ ID 3128, and SEQ ID 2265;         -   (v) 11 lncRNAs of SEQ ID 2540, SEQ ID 0545, SEQ ID 1766, SEQ             ID 3011, SEQ ID 0968, SEQ ID 2371, SEQ ID 1533, SEQ ID 0749,             SEQ ID 0609, SEQ ID 1446, and SEQ ID 2986;         -   (vi) 8 lncRNAs of SEQ1204, SEQ2454, SEQ0334, SEQ1403,             SEQ1089, SEQ2692, SEQ2273, SEQ0502;         -   (vii) 4 lncRNAs of SEQ0097, SEQ1947, SEQ1051 and SEQ2996;             and         -   (viii) lncRNAs in Table 4, Table 5, Table 8, Table 9, Table             12, Table 15, Table 18, Table 19, Table 20, Table 21, Table             22, Table 24, Table 25, Table 28, Table 29, Table 32, Table             33, Table 34, Table 35, Table 36, Table 37, Table 38, Table             39, Table 40, and/or Table 41.     -   1.21 Any of the preceding methods, wherein the expression level         of lncRNA (e.g., SEQ ID NO: 1-SEQ ID NO: 3238) is compared to a         control.     -   1.22 Any of the preceding methods, wherein cardiac disorder can         be selected from the group consisting of: pathologies or         abnormalities related to heart failure (HF) e.g., left and right         ventricle dilatation/dysfunction, reduced ejection fraction         (HFrEF), independently from HF etiology: ICM (Ischemic         HF—related with coronary artery disease, myocardial infarction,         etc.) vs Non-ICM (Non-Ischemic HF—related with myocarditis,         cardiac toxicity, arrhythmia, hypertension, congenital heart         defects, diabetic, idiopathic cardiomyopathy or others).

The invention also provides Method 2. Method 2 is a method for monitoring treatment efficacy in a subject suffering from a cardiac disease or disorder and receiving a pharmaceutical cardiac therapy, the method comprising

-   -   a.) administering a pharmaceutical to a subject suffering from         cardiac injury;     -   b.) obtaining a sample (e.g., a biological sample) from the         subject;     -   c.) detecting the level of expression of one or more lncRNAs         (e.g., having a sequence selected from the group consisting of         SEQ ID NO1 to SEQ ID NO 3238, isoforms thereof, fragment thereof         and variant sharing at least 80% nucleotide sequence homology)         in the sample, wherein the expression level of lncRNA is         compared to a control; and     -   d.) determining the the level of expression of one or more         lncRNAs, wherein the level of expression of said one or more         lncRNAs indicates the efficacy of the treatment,     -   with the proviso that the one or more lncRNAs, fragments         thereof, isoforms thereof and variants sharing at least 80%         nucleotide sequence identity thereto listed in Table 1 are not         part of the present invention.

In various aspects, Method 2 includes the following:

-   -   2.1 Method 2, wherein the level of expression of one or more         said lncRNAs indicates that the subject has developed or is at         risk of developing a cardiac disorder despite the administration         of a pharmaceutical.     -   2.2 Method 2 or 2.1, wherein cardiac disorder is selected from         the group consisting of: pathologies or abnormalities with         Interventricular Septal Thickness (IVS), heart failure (e.g.,         left and right ventricle dilatation/dysfunction), EF, LVID, MI,         HFrEF, myocardial infarction, myocarditis (e.g., viral         myocarditis), cardiac toxicity, brachycardia, arrhythmia,         congenital heart defects, hypertension, diabetic cardiomyopathy,         idiopathic and dilated cardiomyopathy, pathologies characterized         by malformation, pathologies characterized by tissue remodeling,         pathologies characterized by affected function, pathologies         characterized by disorders of the right heart, pathologies         characterized by arrhythmias, pathologies characterized by         intoxication, pathologies characterized by cancer, pathologies         characterized by neurologic disorders, pathologies characterized         by trauma, pathologies characterized by a change in hemodynamic,         pathologies characterized by vascular disorders altering cardiac         functions such as Coronary artery disease (CAD), and pathologies         resulted from cardiac dysfunction/disorders inducing ischemic         (embolic/thrombotic) stroke.     -   2.3 The method of Method 2, 2.1, or 2.2, wherein the diagnosis         step includes predicting the development of heart failure in a         subject having suffered AMI, the method comprising determining         the level of expression, in a biological sample derived from         said subject, of one or more lncRNAs of the invention or         calculating differential expression of one of more lncRNAs         compared to one or more lncRNAs in the same biological sample,         wherein the level of expression or the differential expression         of one or more said lncRNAs predicts the risk for the subject to         develop HF.     -   2.4 The method of any of Method 2-2.3, wherein the method         optionally further comprises the step of administering at least         one pharmaceutical to the subject depending on the efficacy of         the treatment.     -   2.5 The method of any of Method 2-2.4, wherein the level of         expression refers to the differential expression of lncRNAs, the         presence of lncRNAs, or the absence of lncRNAs.     -   2.6 The method of any of the preceding methods, wherein the         subject has been previously diagnosed with Heart Failure (e.g.,         congestive heart failure)     -   2.7 Any of the preceding methods, wherein the biological sample         is selected from the group consisting of: whole blood, serum,         plasma, semen, saliva, tears, urine, fecal material, sweat,         buccal smears, skin, cardiac tissue, liver, brain tissue,         amniotic fluid, nerve tissue and hair (e.g, wherein the sample         is preferably plasma or cardiac tissue).     -   2.8 Any of the preceding methods, wherein the lncRNA expression         levels are measured by technique selected from the group         consisting of: Si nuclease protection assay, microarray         analysis, polymerase chain reaction (PCR), hybridization         technologies, reverse transcriptase polymerase chain reaction         (RT-PCR), Northern blot, serial analysis of gene expression         (SAGE), immunoassay, and mass spectrometry.     -   2.9 Any of the preceding methods, wherein the lncRNA expression         level is detected using a singleplexed or multiplexed method         selected from a group consisting of: fluorescence, luminescence,         radio-marking, next generation sequencing and coded microdisks.     -   2.10 Any of the preceding methods further comprising         administering a pharmaceutical composition which modulates one         or more lncRNAs, wherein the pharmaceutical composition is         selected from the group consisting of: a chemical agent, a RNA         mimic, an antibody, an engineered protease, a CRISPR based         technology and enzymatically active RNA.     -   2.11 The method of 2.10, wherein the enzymatically active RNA is         selected from the group consisting of: a miRNA, a siRNA, a         piRNA, a hnRNA, a snRNA, esiRNA, shRNA, decoys, RNA aptamers and         an antisense oligonucleotide.     -   2.12 Any of the preceding methods, wherein the expression level         of the lncRNAs of the invention are determined by measuring the         levels of cDNAs, amplified RNAs or DNAs or quantities of DNA         probes, or other molecules that are indicative of the expression         level of the lncRNA.     -   2.13 Any of the preceding methods, wherein the lncRNA which is         detected is selected from any of SEQ ID NO: 1-SEQ ID NO: 3238.     -   2.14 Any of the preceding methods, wherein the lncRNA which is         detected is selected from selected from the group consisting of:         -   (i) 15 lncRNAs of SEQ ID 1204, SEQ ID 1736, SEQ ID 0544, SEQ             ID 0915, SEQ ID2368, SEQ ID 1595, SEQ ID 2382, SEQ ID 0859,             SEQ ID 3112, SEQ ID 1869, SEQ ID 1406, SEQ ID 0043, SEQ ID             0363, SEQ ID 0069 and SEQ ID 1947;         -   (ii) 11 lncRNAs of SEQ ID 2373, SEQ ID 1748, SEQ ID 3112,             SEQ ID 1231, SEQ ID 0664, SEQ ID 1686, SEQ ID 0791, SEQ ID             2126, SEQ ID 2750, SEQ ID 3010, and SEQ ID 2241;         -   (iii)14 lncRNAs of SEQ ID 2150, SEQ ID 1534, SEQ ID 0311,             SEQ ID 2952, SEQ ID 2838, SEQ ID 1437, SEQ ID 1297, SEQ ID             1059, SEQ ID 1465, SEQ ID 2826, SEQ ID 0180, SEQ ID 0538,             SEQ ID 0258, and SEQ ID 2273;         -   (iv)20 lncRNAs of SEQ ID 0190, SEQ ID 0359, SEQ ID 0776, SEQ             ID 1421, SEQ ID 1795, SEQ ID 0477, SEQ ID 1511, SEQ ID 0435,             SEQ ID 1418, SEQ ID 1025, SEQ ID 0265, SEQ ID 1311, SEQ ID             2540, SEQ ID 2323, SEQ ID 3011, SEQ ID 2447, SEQ ID 2863,             SEQ ID 2697, SEQ ID 3128, and SEQ ID 2265;         -   (v) 11 lncRNAs of SEQ ID 2540, SEQ ID 0545, SEQ ID 1766, SEQ             ID 3011, SEQ ID 0968, SEQ ID 2371, SEQ ID 1533, SEQ ID 0749,             SEQ ID 0609, SEQ ID 1446, and SEQ ID 2986;         -   (vi) 8 lncRNAs of SEQ1204, SEQ2454, SEQ0334, SEQ1403,             SEQ1089, SEQ2692, SEQ2273, SEQ0502;         -   (vii) 4 lncRNAs of SEQ0097, SEQ1947, SEQ1051 and SEQ2996;             and         -   (viii) lncRNAs in Table 4, Table 5, Table 8, Table 9, Table             12, Table 15, Table 18, Table 19, Table 20, Table 21, Table             22, Table 24, Table 25, Table 28, Table 29, Table 32, Table             33, Table 34, Table 35, Table 36, Table 37, Table 38, Table             39, Table 40, and/or Table 41.     -   2.15 Any of the preceding methods, wherein cardiac disorder can         be selected from the group consisting of: pathologies or         abnormalities related to heart failure (HF) e.g., left and right         ventricle dilatation/dysfunction, reduced ejection fraction         (HFrEF), independently from HF etiology: ICM (Ischemic         HF—related with coronary artery disease, myocardial infarction,         etc.) vs Non-ICM (Non-Ischemic HF—related with myocarditis,         cardiac toxicity, arrhythmia, hypertension, congenital heart         defects, diabetic, idiopathic cardiomyopathy or others).

The invention also provides for Method 3. Method 3 is a method for diagnosing drug-induced cardiac toxicity in a subject receiving a pharmaceutical composition, wherein the method comprises

-   -   a.) obtaining a sample from the subject;     -   b.) measuring the level of expression, (e.g., in a biological         sample derived from said subject) of one or more lncRNAs of the         invention from the sample     -   c.) diagnosing the subject as having a cardiac toxicity from the         pharmaceutical composition depending upon the level of         expression of one or more said lncRNAs (e.g, wherein the lncRNA         is one or more sequences selected from SEQ ID NO: 1 to SEQ ID         NO: 3238),     -   with the proviso that the one or more lncRNAs, fragments         thereof, isoforms thereof and variants sharing at least 80%         nucleotide sequence identity thereto listed in Table 1 are not         part of the present invention.

The invention also provides for Method 4. Method 4 is a method of detecting one or more lncRNAs (e.g., lncRNAs having a sequence selected from the group consisting of SEQ ID NO 1 to SEQ ID NO 3238) useful for Method 1 et seq, Method 2 et seq, and Method 3 et seq. In one aspect, the method comprises the step of obtaining the lncRNA from a human biological sample (e.g., a human plasma sample). The sample can be any biological sample as described in Method 1 et seq, Method 2 et seq, and Method 3 et seq. Method 4 comprises:

-   -   a.) obtaining a sample (e.g., biological sample) from a subject;         and     -   b.) measuring the expression level of the lncRNA (e.g, wherein         the lncRNA is detected by sequencing (e.g.,next generation         sequencing), S1 nuclease protection assay, microarray analysis,         polymerase chain reaction (PCR), hybridization technologies,         reverse transcriptase polymerase chain reaction (RT-PCR),         Northern blot, serial analysis of gene expression (SAGE),         immunoassay, and mass spectrometry) (e.g, wherein the lncRNA is         one or more sequences selected from SEQ ID NO: 1 to SEQ ID NO:         3238),     -   with the proviso that the lncRNAs, fragments thereof, isoforms         thereof and variants sharing at least 80% nucleotide sequence         identity thereto listed in Table 1 are not part of the present         invention.

In various aspects, Method 4 includes the following:

-   -   4.1 Method 4, wherein the expression level of the lncRNA is         measured by sequencing (e.g., next generation sequencing).     -   4.2 The method of any of the preceding methods, wherein         measuring the expression level of the lncRNA comprises the steps         of:         -   (i) extracting RNA from the sample (e.g., blood sample),         -   (ii) converting the RNA to cDNA,         -   (iii) optionally, amplifying the cDNA by PCR, and         -   (iv) sequencing the cDNA.     -   4.3 The method of any of the preceding methods further         comprising a step of capturing and enriching extracted RNA or         cDNA corresponding to lncRNAs of interest prior to sequencing,         comprising the steps of:         -   (1) hybridizing extracted RNA or cDNA to oligonucleotide             probes specific to lncRNAs of interest (e.g.,             oligonucleotide probes comprising a sequence complementary             to a region of lncRNAs of interest) under a condition             allowing for hybridization of the probes and RNA or cDNA             corresponding to lncRNAs of interest to form probe-target             nucleic acid complexes, and         -   (2) purifying the probe-target nucleic acid complexes.     -   4.4 The method of Method 4.3 wherein oligonucleotide probes are         hybridized to cDNA.     -   4.5 The method of any of Methods 4.3-4.4 wherein the         oligonucleotide probe is biotinylated and purifying the         probe-target nucleic acid complexes comprises binding the         probe-target nucleic acid complexes to a streptavidin-coated         substrate.     -   4.6 The method of Method 4.5 wherein the streptavidin-coated         substrate is a streptavidin coated magnetic particle, e.g., T1         streptavidin coated magnetic bead.     -   4.7 The method of any of the preceding methods wherein the         sample is blood sample.     -   4.8 Any of the preceding methods, wherein the lncRNA which is         detected is selected from selected from the group consisting of:         -   (i) 15 lncRNAs of SEQ ID 1204, SEQ ID 1736, SEQ ID 0544, SEQ             ID 0915, SEQ ID2368, SEQ ID 1595, SEQ ID 2382, SEQ ID 0859,             SEQ ID 3112, SEQ ID 1869, SEQ ID 1406, SEQ ID 0043, SEQ ID             0363, SEQ ID 0069 and SEQ ID 1947;         -   (ii) 11 lncRNAs of SEQ ID 2373, SEQ ID 1748, SEQ ID 3112,             SEQ ID 1231, SEQ ID 0664, SEQ ID 1686, SEQ ID 0791, SEQ ID             2126, SEQ ID 2750, SEQ ID 3010, and SEQ ID 2241;         -   (iii) 14 lncRNAs of SEQ ID 2150, SEQ ID 1534, SEQ ID 0311,             SEQ ID 2952, SEQ ID 2838, SEQ ID 1437, SEQ ID 1297, SEQ ID             1059, SEQ ID 1465, SEQ ID 2826, SEQ ID 0180, SEQ ID 0538,             SEQ ID 0258, and SEQ ID 2273;         -   (iv) 20 lncRNAs of SEQ ID 0190, SEQ ID 0359, SEQ ID 0776,             SEQ ID 1421, SEQ ID 1795, SEQ ID 0477, SEQ ID 1511, SEQ ID             0435, SEQ ID 1418, SEQ ID 1025, SEQ ID 0265, SEQ ID 1311,             SEQ ID 2540, SEQ ID 2323, SEQ ID 3011, SEQ ID 2447, SEQ ID             2863, SEQ ID 2697, SEQ ID 3128, and SEQ ID 2265;         -   (v) 11 lncRNAs of SEQ ID 2540, SEQ ID 0545, SEQ ID 1766, SEQ             ID 3011, SEQ ID 0968, SEQ ID 2371, SEQ ID 1533, SEQ ID 0749,             SEQ ID 0609, SEQ ID 1446, and SEQ ID 2986;         -   (vi) 8 lncRNAs of SEQ1204, SEQ2454, SEQ0334, SEQ1403,             SEQ1089, SEQ2692, SEQ2273, SEQ0502;         -   (vii) 4 lncRNAs of SEQ0097, SEQ1947, SEQ1051 and SEQ2996;             and         -   (viii) lncRNAs in Table 4, Table 5, Table 8, Table 9, Table             12, Table 15, Table 18, Table 19, Table 20, Table 21, Table             22, Table 24, Table 25, Table 28, Table 29, Table 32, Table             33, Table 34, Table 35, Table 36, Table 37, Table 38, Table             39, Table 40, and/or Table 41.

The invention also provides for Method 5. Method 5 is a method for identifying lncRNA from a sample (e.g., a biological sample as described in any of Method 1 et seq, Method 2 et seq, and Method 3 et seq.), wherein the lncRNA can be used to treat, diagnose, and/or predict primary and secondary cardiac disorder(s) in a subject. The method comprises

-   -   a.) isolating total RNA from the biological sample (e.g. cardiac         biopsy, serum, or plasma)     -   b.) sequencing total RNA from the sample and determining which         are lncRNA; and     -   c.) comparing the expression (e.g., either relative levels or         presence or absence) of lncRNA to a control;     -   wherein the expression of the lncRNA, compared to a control,         means that the lncRNA can be indicative of primary and secondary         cardiac disorder(s) in a subject, with the proviso that the one         or more lncRNAs, fragments thereof, isoforms thereof and         variants sharing at least 80% nucleotide sequence identity         thereto listed in Table 1 are not part of the present invention.

Method 5 uses any detection method described in Method 1 et seq, Method 2, et seq, Method 3, et seq., and/or Method 4 et seq.

In still a further aspect, the present invention also encompasses a diagnostic/prognostic kit for carrying out any of the previously cited methods (any of Method 1 et seq, Method 2, et seq, Method 3, et seq., and/or Method 4 et seq and/or Method 5 et seq.). In some embodiments, the diagnostic/prognostic kit comprises one or more oligonucleotide probes specific to lncRNAs of interest (e.g., lncRNAs selected from the group consisting of SEQ ID NO1 to SEQ ID NO 3238, isoforms thereof, fragment thereof and variant sharing at least 80% nucleotide sequence homology) and a reagent for purifying the probe-target nucleic acid complexes. The oligonucleotide probes comprise a sequence complementary to a region of the lncRNAs of interest. The oligonucleotide probes may be DNA or RNA. The oligonucleotide probes are preferably DNA. The length of oligonucleotide probes may be from 30 to 80 nucleotides, e.g., from 40 to 70, from 40 to 60, or about 50 nucleotides. In a preferred embodiment, the oligonucleotide probes are biotinylated and the reagent for purifying the probe-target complexes is a streptavidin-coated substrate, e.g, a streptavidin-coated magnetic particle, e.g., T1 streptavidin coated magnetic bead.

In some embodiments, the diagnostic/prognostic kit comprises one or more oligonucleotide probes specific to one or more lncRNAs (i.e., oligonucleotide probes comprising a sequence complementary to a region of the lncRNAs of interest) selected from any of SEQ ID NO: 1-SEQ ID NO: 3238.

In some embodiments, the diagnostic/prognostic kit comprises one or more oligonucleotide probes specific to one or more lncRNAs selected from the group consisting of:

-   -   (i) 15 lncRNAs of SEQ ID 1204, SEQ ID 1736, SEQ ID 0544, SEQ ID         0915, SEQ ID2368, SEQ ID 1595, SEQ ID 2382, SEQ ID 0859, SEQ ID         3112, SEQ ID 1869, SEQ ID 1406, SEQ ID 0043, SEQ ID 0363, SEQ ID         0069 and SEQ ID 1947;     -   (ii) 11 lncRNAs of SEQ ID 2373, SEQ ID 1748, SEQ ID 3112, SEQ ID         1231, SEQ ID 0664, SEQ ID 1686, SEQ ID 0791, SEQ ID 2126, SEQ ID         2750, SEQ ID 3010, and SEQ ID 2241;     -   (iii) 14 lncRNAs of SEQ ID 2150, SEQ ID 1534, SEQ ID 0311, SEQ         ID 2952, SEQ ID 2838, SEQ ID 1437, SEQ ID 1297, SEQ ID 1059, SEQ         ID 1465, SEQ ID 2826, SEQ ID 0180, SEQ ID 0538, SEQ ID 0258, and         SEQ ID 2273;     -   (iv) 20 lncRNAs of SEQ ID 0190, SEQ ID 0359, SEQ ID 0776, SEQ ID         1421, SEQ ID 1795, SEQ ID 0477, SEQ ID 1511, SEQ ID 0435, SEQ ID         1418, SEQ ID 1025, SEQ ID 0265, SEQ ID 1311, SEQ ID 2540, SEQ ID         2323, SEQ ID 3011, SEQ ID 2447, SEQ ID 2863, SEQ ID 2697, SEQ ID         3128, and SEQ ID 2265;     -   (v) 11 lncRNAs of SEQ ID 2540, SEQ ID 0545, SEQ ID 1766, SEQ ID         3011, SEQ ID 0968, SEQ ID 2371, SEQ ID 1533, SEQ ID 0749, SEQ ID         0609, SEQ ID 1446, and SEQ ID 2986;     -   (vi)8 lncRNAs of SEQ1204, SEQ2454, SEQ0334, SEQ1403, SEQ1089,         SEQ2692, SEQ2273, SEQ0502;     -   (vii) 4 lncRNAs of SEQ0097, SEQ1947, SEQ1051 and SEQ2996; and     -   (viii) lncRNAs in Table 4, Table 5, Table 8, Table 9, Table 12,         Table 15, Table 18, Table 19, Table 20, Table 21, Table 22,         Table 24, Table 25, Table 28, Table 29, Table 32, Table 33,         Table 34, Table 35, Table 36, Table 37, Table 38, Table 39,         Table 40, and/or Table 41.

EXAMPLES Example 1 Identification of lncRNAs of the Invention

The inventors incorporate deep RNA-sequencing of cardiac biopsies starting from total RNA to characterize both coding and non-coding transcriptomes and identify cardiac relevant lncRNA through a multistep analysis procedure. The Inventors use differential expression analysis as well as novel transcript reconstruction and data integration into genome-wide data sets as well as previously characterized predicted human cardiac-specific lncRNA to systematically identify heart-specific lncRNAs. Using the aforementioned techniques, the Inventors can identify 3,238 lncRNAs potentially relevant to cardiac disorders. Indeed, hundreds of known lncRNA are differentially expressed in a control subject compared to a subject suffering from ischemic or dilated cardiomyopathies. The Inventors are able to determine that 1027 novel lncRNAs, including some orthologs predicted in the art, that are differentially expressed and/or cardiac-enriched.

Sample Collection

Cardiac biopsies are obtained from 5 control patients, 11 patients suffering ICM and 10 patients suffering DCM. Biopsies of control hearts are provided from subjects with either head injury (n=2) or subarachnoid haemorrhage (n=3). The protocol is approved by the Local Ethics Committee at Cardinal Stefan Wyszynski Institute of Cardiology (approval number IK-NP-0021-48/846/13 (Apr. 9, 2013). No donors or their relatives completed the National Refusal List. Heart biopsies obtained from the left ventricle are snap-frozen and stored at −80° C. until RNA isolation.

RNA Isolation

Total RNA is extracted from cardiac biopsies using the mirVana isolation kit (Life technologies, Merelbeke, Belgium). Potential contaminating genomic DNA is digested with DNase I (Qiagen, Venlo, The Netherlands). RNA concentration is measured with a Nanodrop spectrophotometer (Nanodrop products, Wilmington, USA) and RNA integrity is verified using a 2100 Bioanalyzer (Agilent technologies, Santa Clara, USA).

Biopsies Sequencing

Sequencing libraries are prepared from 0.5 μg of total RNA using the Illumina TruSeq stranded total RNA library preparation kit combined with the human/mouse/rat RiboZero rRNA removal kit (Illumina Inc. San Diego, USA, C). All steps are performed with the low-throughput protocol and according to the manufacturer's instructions. Briefly, cytoplasmic rRNA are hybridized to biotinylated target-specific oligos and removed using streptavidin coated magnetic beads. rRNA depleted RNA samples are then fragmented by heat digestion with divalent cations (8 minutes, 94° C.) and reverse transcribed into cDNA. To ensure strand specificity, single stranded cDNA is first synthetized using Super-Script II reverse transcriptase (Invitrogen) and random primers in the presence of Actinomycin D, and then converted to double stranded cDNA with the second strand marking mix that incorporates dUTP in place of dTTP. Resulting blunt ended cDNA are purified using AMPure XP magnetic beads. After a 3′end adenylation step, Illumina's adapters ligation is performed. The singled indexed libraries thus obtained are washed twice using AMPure XP beads to remove excess adapters and enriched by PCR (15 cycles). PCR products are purified with a final AMPure XP beads wash and sequencing ready libraries are eluted in 30 μl of resuspension buffer.

For quality control, 1 μl of each library is run on the Agilent Technologies 2100 Bioanalyzer using a DNA 1000 chip according to the manufacturer's recommendations. Absence of adapter dimers is checked and the average library size is determined by a region table. Libraries are quantified by qPCR using the KAPA Library quantification kit for Illumina Platforms (KAPAbiosystems,). Samples are run in duplicate and quantified against a standard curve ranging from 20 to 2.10-4 pM. Library size previously determined on the Bioanalyzer is used for size correction of the calculated concentrations.

All libraries are sequenced with the Illumina NextSeq500 (2×75 bp).

Sequencing Analysis for Known Transcripts

All RNA-seq reads of 26 samples are aligned to human reference genome (hg19) using Tophat 2.1.0 (1). Bowtie index of UCSC reference sequences are downloaded from Illumina iGenomes. The transcript assembly is performed using cufflinks 2.2.1 (1) with −G option and the featureCounts function of Rsubread R package (2). The GTF file is generated by integrating GENCODE comprehensive gene annotation release 19 (3) and human lncRNAs identified by Ounzain et al. (4). Cuffdiff (1) and DESeq2 (5) are respectively used for differential expression analysis. Transcripts with an adjusted p-value<0.05 between controls and failing hearts, or with a p-value<0.05 between ICM and DCM are considered to be differentially expressed.

Pipeline of Novel lncRNA Prediction

De Novo Transcript Assembly

RABT (Reference Annotation Based Transcript) assembly (6) is performed using cufflinks with −g option for 3 control samples, 3 ICM samples and 3 DCM samples. The GTF file is the same as the one used for known transcripts. The cuffcompare (1) program is used to compare the assembled transcripts to the reference annotated GTF file and to generate a new GTF file with all transcripts from 9 samples for further analysis.

Filtering for Novel lncRNAs

Filtering is done on Transfrag class codes generated by cuffcompare, transcript length, number of exons and protein coding potential. Firstly, the transcripts with code ‘i’, ‘j’, ‘o’, ‘u’, ‘x’ and ‘.’ are extracted, all of which could potentially include novel lncRNAs. The ‘i’ category, for example, could contain the lncRNAs entirely within the intron of known genes. Similarly, the ‘j’ category could be long non-coding isoforms of known genes. The ‘o’ category could include novel lncRNAs having generic exonic overlap with known transcripts. The ‘u’ category could be long intergenic non-coding RNAs (lincRNAs). The ‘x’ category could contain novel lncRNAs on the opposite strand of reference genes. The ‘.’ category may be sequences with multiple classifications. The combined GTF file is converted to a BED file using UCSC table browser (7). Following this, only the transcripts with a length of ≥200 nt and with at least 2 exons are kept for the next step. Finally, the BED files of transcripts from the last 2 filtering steps are uploaded to CPAT (Coding-Potential Assessment Tool) (8) to calculate the coding potential score. The transcripts with CPAT scores<0.364 are considered as non-coding. A new GTF file is generated with the final list of selected novel lncRNAs.

Differential Expression of Novel lncRNAs

The cuffdiff (1) is used for all 26 samples with the new GTF file of novel lncRNAs. Transcripts with an adjusted p-value<0.05 are considered to be differentially expressed.

Analysis for Public Dataset

Fastq files of GSE45326 are downloaded from ArrayExpress (9). The dataset includes RNA-seq data of 12 normal human tissues. The paired-end sequencing is performed on ribominus total RNA library. Reads alignment and transcript assembly for known genes are performed as described before. Cufflinks (1) with the GTF file of novel lncRNAs is used to calculate FPKM of novel lncRNAs in each tissue. The transcripts with FPKM≥1 and at least twice higher than the FPKM of any other tissues are considered as cardiac-enriched.

The selection of the lncRNA of the panel is a multistep procedure:

Known transcripts selection.

In a first step, the inventors focused on the identification of known lncRNA that are relevant to cardiac pathophysiology. After data alignment and transcript reconstruction using both Cufflink and features counts using Gencode19, the authors used two distinct tools that use different approaches for differential expression analysis, respectively Cuffdiff and DeSeq2, and only transcripts showing high expression (fragments per kilobase of transcript per million mapped reads (FPKM) FPKM or FPM≥1) in at least half the samples of one group are considered. Differential expression using both tools is analysed in controls vs ICM samples, controls vs DCM samples, as well as ICM vs DCM samples. 80 and 1193 differentially expressed transcripts between any of the groups are identified with Cuffdiff and DeSeq2 analysis respectively. This difference is mainly due to the low number of lncRNA flagged OK by Cuffdiff (ie, neither NOTEST nor HIDATA). As those excluded lncRNA are included in the DeSeq2 analysis, Cuffdiff default settings are not modified. Interestingly, we observed from the DeSeq2 analysis that even if the majority of differentially expressed transcripts in controls vs ICM samples are also differentially expressed in controls vs DCM samples (and vice versa), about one third of them are ICM or DCM specific, illustrating that as the coding transcriptome, the noncoding transcriptome shows features common to a common heart defect (cardiomyopathies) but also specific ones differentiating the physiological bases of this defect (ischemic vs non-ischemic). Moreover, 97 lncRNAs are also differentially expressed between ICM and DCM patients, differentiating the 2 pathologies. Similar observations are made from the Cuffdiff analysis.

The authors also focused on highly expressed non coding transcripts and thus selected 687 lncRNA having a FPKM or FPM≥2 to include in the panel.

In summary, the authors identified 1,835 lncRNA corresponding to 1,501 genes, previously annotated in Gencode19, as relevant for cardiac function.

Predicted Human Orthologs Selection

In order to validate the relevance of the humans orthologs identified by Ounzain et al, the authors realized the same analysis using the GTF file containing the predicted human orthologs as reference for transcripts reconstruction. Surprisingly, the inventors identified few predicted orthologs that are expressed in human tissue: 86 corresponding to 77 genes. Among them, 75 are differentially expressed lncRNA across the control, ICM and DCM groups, 16 highly expressed (FPKM or FPM≥2) lncRNA and 5 of them fitted the 2 criteria. This unexpected low amount of validated predicted human orthologs can in part be explained by the different sequencing approaches used in the 2 studies. Nonetheless, the so identified lncRNAs, shown to be highly tissue and context specific in mice and validated in human cardiac disorders appear to be promising biomarker candidates playing crucial roles in cardiac function regulation.

Cardiac-Enriched Transcripts Selection

As stated in the previous study from Ounzain et al, lncRNA regulating cardiac homeostasis identified in mice are highly context specific but also and importantly, cardiac tissue specific. This led us to look for non-coding transcripts that are enriched in the cardiac tissue compared to others and thus might play important roles in cardiac functions. By comparing public RNA-seq data from 12 human tissues (heart, brain, bladder, colon, breast, skin, lung, ovary, kidney, prostate, liver, muscle), the inventors identified 470 and 24 lncRNA, from known and Human predicted transcripts respectively, that had at least a 2 fold higher expression rate in cardiac tissue than in any other tissue.

Novel Transcripts Selection

The growing interest on lncRNA together with the development of next generation sequencing techniques over the past years has led to a better knowledge of these non-coding transcripts. Nonetheless, non-coding transcripts account for the majority of the human transcriptome and have so far not been completely characterized. The authors thus performed very deep sequencing to allow for discovery of novel transcripts. After de novo transcript reconstruction and transcript selection as detailed in the material and methods, the inventors can identify over 13,000 new transcripts with no coding potential. Among them, they can identify 696 lncRNA differentially expressed between the 3 groups (FDR<0.05) and 810 lncRNA enriched in cardiac tissue. The transcripts having class codes ‘o’, ‘j’ or ‘i’ and highly positively correlated with overlapped known genes are eliminated. (‘i’ category, for example, could contain the lncRNAs entirely within the intron of known genes, the ‘j’ category could be long non-coding isoforms of known genes and the ‘o’ category could include novel lncRNAs having generic exonic overlap with known transcripts). The transcripts with class codes ‘j’ or ‘o’ and overlapping with exons of known protein-coding genes on the same strand are discarded. This resulted in a total number of novel lncRNAs of 755 relevant to cardiac physiology.

In summary, the inventors identified a highly relevant panel of 3,092 cardiac-related lncRNAs. This panel encompasses 2,317 known transcripts here shown to be relevant to cardiac physiology, as well as 755 lncRNA, here described for the first time and relevant to cardiac tissue.

Example 2

LncRNA Detection in Plasma Samples and PCR Validation in Biopsies

Sample Selection: Mitocare Aidbank/

Like miRNA, lncRNA can be released from the original tissue into the body circulation. Thus such markers may be detected in body fluids like whole blood or plasma which facilitates their use in clinics. The expression of four lncRNA previously identified is verified in plasma samples from patients who suffered AMI versus control patients.

Plasma samples from 3 control subjects and 3 subjects who suffered AMI are used. RNA extraction is performed using Norgen Serum/plasma extraction kit according to the manufacturer's instructions. Isolated RNAs are then subjected to reverse transcription using the high capacity cDNA synthesis kit with the following thermal conditions: 25° C. for 10 min, 37° C. for 2 hours, 85° C. for 5 min. Preamplification reactions are prepared using Applied Biosystems preamplication master mix with 0.1× (100 nM) of each of the 4 primers pairs corresponding to the lncRNAs of interest (sequences listed below). 16 preamplification cycles are performed as recommended by the furnisher (50° C. 2 minutes, 96° C. 10 minutes, 40 cycles at 95° C. for 15 seconds and 60° C. for 1 minute). Preamplified products are then diluted 1/20 in TE buffer and quantified by qPCR using the Biorad Ssoadvanced SYBR green kit. Briefly, 15 μl reactions containing 6 ul of each diluted sample are amplified in a 1× ready to use reaction mix containing 500 μl of the diluted sample, 1× biorad reaction mix and and 500 nM sense and reverse primers are amplified on a ABIHT7900 with the following conditions: 30 sec 95° C., 40 cycles of 15 sec at 95° C. denaturation and 30 sec at 60° C. annealing and extension). Relative expression level is determined against a standard curve realized on a 5 log scale.

TABLE 2 Lnc21524Se TTGAATCCTGGCTTTGCTCT Lnc21524As GGAAAGGCAATTGAGTGAGG Lnc23749Se TTGGTCTTTCACCCTTCCTG Lnc23749As GAAAACGTCCTCCCTCCTTC Lnc19889Se ACACGGGAAGCTCTTTGAGA Lnc19889As TCAAGAGGGAAGGATGGATG LncAnx5aSe GAATTTCTGGGGACCTTTCC LncAnx5aAs GCAAAGGGAGAGAAAGCAGA

In FIG. 4, the authors showed that lncRNA are indeed detectable in plasma samples. Moreover expression profile compared to NGS data (lnc21524 identified with NGS need more precision on DE).

Example 3 LncRNA Detection in Serum Samples Using a Total RNA-seq Protocol

Material and Methods:

Quantification of lncRNAs in body fluids like whole blood, serum or plasma is a non-invasive way to develop a diagnostic test to use in clinics. The expression of circulating lncRNA released by the tissues was studied in serum samples from patients with AMI and control subjects. Serum samples collected at discharge of patient between D3 and D5 from 30 patients with AMI from the MitoCare cohort were used for lncRNA profiling. Mitocare is a multicenter, randomized, double-blind, placebo controlled study. The study population includes AMI patients undergoing PCI (Percutaneous Coronary Intervention), older than 18 years. The primary endpoint is the level of left ventricular ejection fraction (LVEF) less than 40% at 1 month. Patients demographics are presented in Table 3. Control serum samples were selected from subjects of ADDIA Chronobiological study.

TABLE 3 Demographic data of Mitocare samples: Group 1 Group 2 Group 3 EF <40 41-50 >50 Nb 10 10  10 Age 64.0 64.2 60.9 Male 80% 80% 70% BMI 27.4 28.3 27.6 Systolic Blood 103.5 116.9  113.6 Pressure Diastolic Blood 67.4 70.2 66.5 Pressure Heart Rate 83.3 75.9 69.3

Serum Samples Sequencing

RNA is extracted from 1.5 ml of serum, using Norgen Serum extraction and RNA Clean-Up and Concentration Micro-Elute Kits according to the manufacturer's instructions. Sequencing libraries are prepared from the total amount of extracted RNA, using the Illumina TruSeq stranded total RNA library preparation kit combined with the human/mouse/rat RiboZero rRNA removal kit (Illumina Inc. San Diego, USA, C). All steps are performed with the low-throughput protocol and according to the manufacturer's instructions, with no fragmentation step. Briefly, cytoplasmic rRNA are hybridized to biotinylated target-specific oligos and removed using streptavidin coated magnetic beads. rRNA depleted RNA samples are then reverse transcribed into cDNA. To ensure strand specificity, single stranded cDNA is first synthetized using Super-Script II reverse transcriptase (Invitrogen) and random primers in the presence of Actinomycin D, and then converted to double stranded cDNA with the second strand marking mix that incorporates dUTP in place of dTTP. Resulting blunt ended cDNA are purified using AMPure XP magnetic beads. After a 3′end adenylation step, Illumina's adapters ligation is performed. So obtained singled indexed libraries are washed twice using AMPure XP beads to remove excess adapters and enriched by PCR (15 cycles). PCR products are purified with a final AMPure XP beads wash and sequencing ready libraries are eluted in 30 μl of resuspension buffer.

For quality control, 1 μl of each library is run on the Agilent Technologies 2100 Bioanalyzer using a DNA 1000 chip according to the manufacturer's recommendations. Absence of adapter dimers is checked and the average library size is determined by a region table. Libraries are quantified on Qubit 2.0 using Qubit dsDNA High Sensitivity assay kit (Invitrogen). Library size previously determined on the Bioanalyzer is used to calculate molar concentrations from mass concentrations.

All libraries are sequenced with the Illumina NextSeq500 (2×75 bp).

Sequencing Analysis for the 3238 lncRNAs

RNA-seq data analysis is performed using Partek Flow (Partek Inc., St Louis, Mo., USA build 6). The pre-alignment QA/QC module of Partek Flow is used to visualize the read quality of the FASTQ files. All reads are examined. The raw FASTQ files are trimmed at the 3′ end in function of their quality score (Phred score). The parameters used are an end minimum quality level of 30 and a minimum trimmed read length of 50. Unaligned reads are mapped using the Homo sapiens hg19 genome and using as guide a GTF file with the patented lncRNA annotation. This mapping is done using the software STAR version 2.5.3. The default parameters are used. The post-alignment QC module of Partek Flow is used to visualize the average base quality score per position as well as the mapping quality per alignment. The mapped reads are quantified using the GTF file with the patented lncRNA annotation for quantification using the Partek Expectation/Maximization (E/M) algorithm. The default parameters are used. The transcript counts are normalized by CPM (counts per million). Only transcripts showing high expression (CPM≥10) in at least half the samples of one group are considered.

Statistical Analysis and Predictive Modelling

For the statistical analysis, samples are grouped into 2 groups based on the left ventricular ejection fraction (LVEF) measured by echocardiography at 1-month after the PCI. To identify differentially expressed lncRNA, a statistical analysis is performed using a non-parametric Wilcoxon-Mann-Whitney test and a parametric T-test. A lncRNA with a p-value≤0.05 is considered as differentially expressed.

In order to build classification models for the 2 classifications, the Classification for MicroArrays (CMA) package of R (Slawski et al, 2008) with a leave-one-out cross-validation is used. The algorithms used for this predictive modelling are (a) random forest, (b) linear discriminant analysis and (c) naïve Bayes.

Results:

Comparison Between Low LVEF (LVEF≤40) and High LVEF (LVEF>40)

First, samples were grouped into 2 groups by a dichotomized variable: 1-month LVEF<40% considered as LV dysfunction (Ventricular remodeling) and 1-month LVEF>40% considered as preserved LV function. The volcano plot showed the differential expression of lncRNA. 192 lncRNAs are differentially expressed and among these, 20 lncRNAs are differentially expressed and have a fold change>2 or <0.5 between the low LVEF (LVEF≤40) and the high LVEF (LVEF>40) groups. The p-value and the fold-change of these lncRNA are listed in the Table 4. 316 lncRNAs which have a P<0.05 and/or an individual AUC>0.7 or <0.3 are listed in Table 5.

TABLE 4 List of 20 lncRNAs which are differentially expressed between the low LVEF group (LVEF ≤ 40) and the high LVEF group (LVEF > 40) lncRNA p-value Fold change lncRNA p-value Fold change SEQ0930 0.03736 2.042 SEQ1837 0.04199 0.416 SEQ0821 0.03299 0.491 SEQ0527 0.01436 0.487 SEQ1196 0.00653 2.648 SEQ1167 0.01803 0.296 SEQ0664 0.00660 0.441 SEQ0153 0.04675 2.333 SEQ2642 0.04102 2.623 SEQ1757 0.04483 2.224 SEQ1910 0.04224 2.669 SEQ1719 0.02190 0.367 SEQ1239 0.01161 0.475 SEQ1650 0.00217 0.487 SEQ0243 0.04133 0.490 SEQ0051 0.01192 52.864 SEQ2368 0.00240 0.443 SEQ1410 0.00818 2.953 SEQ0283 0.01599 2.363 SEQ2699 0.02230 2.072

TABLE 5 List of 316 IncRNAs which are differentially expressed and/or have an AUC >0.7 or <0.3 between the low LVEF group (LVEF ≤ 40) and the high LVEF group (LVEF > 40) IncRNA p-value AUC SEQ0005 0.033 0.755 SEQ0033 0.131 0.715 SEQ0037 0.061 0.73 SEQ0042 0.119 0.715 SEQ0043 0.068 0.175 SEQ0051 0.012 0.225 SEQ0069 0.168 0.255 SEQ0075 0.028 0.745 SEQ0119 0.021 0.33 SEQ0120 0.046 0.735 SEQ0136 0.026 0.71 SEQ0141 0.05 0.28 SEQ0153 0.047 0.328 SEQ0163 0.083 0.285 SEQ0169 0.042 0.73 SEQ0172 0.045 0.74 SEQ0173 0.046 0.76 SEQ0189 0.024 0.755 SEQ0190 0.043 0.73 SEQ0199 0.004 0.83 SEQ0208 0.027 0.283 SEQ0216 0.087 0.735 SEQ0226 0.083 0.72 SEQ0243 0.041 0.73 SEQ0244 0.01 0.24 SEQ0283 0.016 0.27 SEQ0290 0.079 0.715 SEQ0312 0.065 0.25 SEQ0321 0.022 0.815 SEQ0334 0.017 0.785 SEQ0339 0.042 0.71 SEQ0363 0.001 0.87 SEQ0366 0.216 0.3 SEQ0383 0.052 0.7 SEQ0386 0.113 0.715 SEQ0388 0.116 0.71 SEQ0392 0.029 0.74 SEQ0398 0.027 0.795 SEQ0405 0.051 0.73 SEQ0420 0.06 0.72 SEQ0454 0.06 0.295 SEQ0493 0.05 0.715 SEQ0495 0.072 0.755 SEQ0502 0.065 0.75 SEQ0538 0.083 0.715 SEQ0544 0.002 0.825 SEQ0552 0.039 0.775 SEQ0560 0.063 0.725 SEQ0565 0.064 0.7 SEQ0586 0.032 0.775 SEQ0615 0.008 0.825 SEQ0638 0.017 0.77 SEQ0643 0.072 0.725 SEQ0664 0.007 0.815 SEQ0677 0.073 0.74 SEQ0685 0.014 0.79 SEQ0688 0.079 0.72 SEQ0702 0.035 0.77 SEQ0745 0.029 0.725 SEQ0748 0.052 0.71 SEQ0753 0.063 0.7 SEQ0781 0.015 0.76 SEQ0796 0.065 0.7 SEQ0821 0.033 0.738 SEQ0858 0.129 0.7 SEQ0861 0.082 0.715 SEQ0866 0.036 0.735 SEQ0904 0.042 0.73 SEQ0910 0.054 0.72 SEQ0915 0.009 0.81 SEQ0917 0.025 0.765 SEQ0925 0.037 0.72 SEQ0930 0.037 0.3 SEQ0935 0.039 0.72 SEQ0944 0.055 0.725 SEQ0948 0.073 0.28 SEQ0959 0.029 0.745 SEQ0994 0.12 0.715 SEQ1001 0.11 0.713 SEQ1004 0.041 0.715 SEQ1014 0.037 0.74 SEQ1036 0.038 0.25 SEQ1040 0.134 0.72 SEQ1042 0.046 0.31 SEQ1046 0.006 0.785 SEQ1075 0.069 0.7 SEQ1081 0.055 0.73 SEQ1089 0.045 0.765 SEQ1094 0.013 0.78 SEQ1095 0.089 0.74 SEQ1113 0.037 0.725 SEQ1114 0.063 0.71 SEQ1127 0.061 0.715 SEQ1171 0.106 0.745 SEQ1179 0.049 0.28 SEQ1182 0.032 0.73 SEQ1198 0.016 0.765 SEQ1204 0 0.88 SEQ1205 0.001 0.8 SEQ1214 0.045 0.71 SEQ1231 0.037 0.3 SEQ1240 0.044 0.74 SEQ1271 0.109 0.715 SEQ1276 0.053 0.725 SEQ1281 0.016 0.22 SEQ1286 0.409 0.71 SEQ1301 0.087 0.71 SEQ1319 0.048 0.32 SEQ1329 0.006 0.245 SEQ1340 0.084 0.283 SEQ1347 0.065 0.705 SEQ1348 0.013 0.275 SEQ1356 0.099 0.705 SEQ1373 0.024 0.215 SEQ1377 0.121 0.7 SEQ1385 0.117 0.71 SEQ1391 0.133 0.71 SEQ1398 0.004 0.195 SEQ1403 0.018 0.775 SEQ1404 0.109 0.705 SEQ1406 0.083 0.74 SEQ1410 0.008 0.235 SEQ1412 0.042 0.775 SEQ1420 0.042 0.75 SEQ1428 0.006 0.225 SEQ1442 0.026 0.715 SEQ1444 0.057 0.29 SEQ1449 0.089 0.7 SEQ1454 0.098 0.708 SEQ1462 0.071 0.728 SEQ1468 0.002 0.81 SEQ1483 0.041 0.27 SEQ1518 0.154 0.71 SEQ1528 0.018 0.735 SEQ1556 0.102 0.72 SEQ1564 0.018 0.765 SEQ1576 0.051 0.725 SEQ1583 0.083 0.715 SEQ1595 0.152 0.715 SEQ1601 0.007 0.24 SEQ1618 0.056 0.275 SEQ1626 0.004 0.785 SEQ1632 0.048 0.305 SEQ1638 0.091 0.275 SEQ1656 0.083 0.725 SEQ1667 0.022 0.735 SEQ1674 0.006 0.8 SEQ1683 0.024 0.745 SEQ1692 0.084 0.745 SEQ1693 0.05 0.7 SEQ1705 0.12 0.295 SEQ1707 0.016 0.77 SEQ1712 0.063 0.71 SEQ1715 0.01 0.665 SEQ1719 0.022 0.77 SEQ1726 0.006 0.23 SEQ1732 0.002 0.855 SEQ1733 0.046 0.74 SEQ1737 0.037 0.315 SEQ1746 0.137 0.705 SEQ1757 0.045 0.338 SEQ1793 0.13 0.71 SEQ1804 0.056 0.75 SEQ1809 0.05 0.305 SEQ1818 0.022 0.74 SEQ1819 0.031 0.8 SEQ1820 0.154 0.255 SEQ1837 0.042 0.748 SEQ1842 0.035 0.735 SEQ1853 0.194 0.705 SEQ1869 0.051 0.755 SEQ1910 0.042 0.37 SEQ1926 0.061 0.755 SEQ1938 0.058 0.71 SEQ1942 0.048 0.72 SEQ1947 0.091 0.733 SEQ1950 0.156 0.71 SEQ1954 0.174 0.29 SEQ1979 0.04 0.72 SEQ1983 0.002 0.865 SEQ2026 0.031 0.71 SEQ2049 0.012 0.78 SEQ2053 0.121 0.71 SEQ2061 0.068 0.29 SEQ2074 0.004 0.215 SEQ2100 0.007 0.78 SEQ2114 0.062 0.725 SEQ2121 0.058 0.725 SEQ2126 0.032 0.25 SEQ2157 0.049 0.695 SEQ2162 0.051 0.705 SEQ2190 0.109 0.705 SEQ2209 0.074 0.81 SEQ2216 0.077 0.71 SEQ2240 0.069 0.27 SEQ2253 0.006 0.19 SEQ2260 0.063 0.285 SEQ2273 0.064 0.72 SEQ2274 0.043 0.27 SEQ2282 0.023 0.235 SEQ2286 0.06 0.295 SEQ2287 0.048 0.27 SEQ2288 0.007 0.2 SEQ2294 0.086 0.705 SEQ2299 0.015 0.765 SEQ2314 0.019 0.735 SEQ2320 0.005 0.83 SEQ2344 0.024 0.72 SEQ2349 0.1 0.275 SEQ2352 0.033 0.32 SEQ2353 0.075 0.705 SEQ2360 0.045 0.295 SEQ2368 0.002 0.85 SEQ2373 0 0.85 SEQ2374 0.016 0.245 SEQ2377 0.036 0.73 SEQ2382 0.012 0.835 SEQ2385 0.05 0.72 SEQ2402 0.003 0.82 SEQ2405 0.102 0.7 SEQ2407 0.1 0.275 SEQ2411 0.047 0.7 SEQ2454 0.015 0.755 SEQ2457 0.027 0.74 SEQ2461 0.031 0.245 SEQ2466 0.138 0.71 SEQ2470 0.001 0.15 SEQ2472 0.032 0.255 SEQ2478 0.02 0.23 SEQ2484 0.038 0.28 SEQ2485 0.026 0.375 SEQ2501 0.008 0.805 SEQ2502 0.049 0.745 SEQ2518 0.091 0.29 SEQ2521 0.015 0.3 SEQ2523 0.019 0.76 SEQ2540 0.019 0.745 SEQ2544 0.022 0.255 SEQ2560 0.075 0.705 SEQ2567 0.026 0.745 SEQ2593 0.057 0.29 SEQ2605 0.044 0.32 SEQ2618 0.032 0.215 SEQ2622 0.118 0.29 SEQ2631 0.027 0.27 SEQ2644 0.054 0.285 SEQ2657 0.033 0.65 SEQ2658 0.069 0.27 SEQ2677 0.037 0.7 SEQ2684 0.005 0.185 SEQ2692 0.062 0.28 SEQ2695 0.026 0.24 SEQ2696 0.07 0.265 SEQ2697 0.045 0.725 SEQ2698 0.052 0.705 SEQ2699 0.022 0.325 SEQ2702 0.041 0.34 SEQ2703 0.005 0.805 SEQ2715 0.032 0.25 SEQ2720 0.054 0.7 SEQ2726 0.04 0.735 SEQ2750 0.047 0.735 SEQ2752 0.025 0.695 SEQ2753 0.06 0.735 SEQ2785 0.039 0.275 SEQ2794 0.035 0.32 SEQ2800 0.18 0.705 SEQ2825 0.11 0.7 SEQ2830 0.018 0.72 SEQ2833 0.158 0.295 SEQ2853 0.003 0.785 SEQ2875 0.047 0.28 SEQ2882 0.037 0.24 SEQ2896 0.02 0.27 SEQ2912 0.119 0.7 SEQ2921 0.06 0.295 SEQ2922 0.015 0.25 SEQ2928 0.016 0.775 SEQ2930 0.046 0.295 SEQ2960 0.057 0.28 SEQ2971 0.024 0.755 SEQ2973 0.039 0.28 SEQ2974 0.067 0.7 SEQ2982 0.007 0.22 SEQ2998 0.022 0.765 SEQ3002 0.04 0.69 SEQ3006 0.023 0.77 SEQ3007 0.041 0.26 SEQ3013 0.05 0.725 SEQ3040 0.066 0.705 SEQ3048 0.017 0.31 SEQ3066 0.009 0.805 SEQ3070 0.052 0.3 SEQ3080 0.045 0.25 SEQ3085 0.034 0.725 SEQ3112 0.029 0.265 SEQ3113 0.024 0.28 SEQ3118 0.085 0.265 SEQ3128 0.034 0.295 SEQ3129 0.005 0.19 SEQ3133 0.019 0.765 SEQ3141 0.126 0.74 SEQ3142 0.107 0.295 SEQ3143 0.025 0.305 SEQ3153 0.005 0.795 SEQ3156 0.051 0.71 SEQ3170 0.044 0.295 SEQ3180 0.039 0.725 SEQ3184 0.024 0.28 SEQ3187 0.024 0.33 SEQ3200 0.049 0.26 SEQ3203 0.002 0.19 SEQ3204 0.017 0.75 SEQ3210 0.044 0.665 SEQ3221 0.002 0.135 SEQ3230 0.036 0.3

For this classification, the variable selection was performed by using a Random Forest model. A combination of 15 pre-selected lncRNAs through a Random Forest Classifier (Table 6) is the best predictive model obtained here. The lncRNAs were selected using a random forest algorithm. This model has an area under the receiver-operating characteristic curve (AUC) of 0.988, an accuracy of 0.9, a sensitivity of 0.8, a specificity of 0.95, a Positive Predictive Value (PPV) of 0.889 and Negative Predictive Value (PNV) of 0.905. The confusion matrix is presented in Table 7.

TABLE 6 List of 15 pre-selected lncRNAs through a Random Forest Classifier for the classification low LVEF (LVEF ≤ 40) and high LVEF (LVEF > 40) lncRNA Rank in the model SEQ1204 1 SEQ1736 2 SEQ0544 3 SEQ0915 4 SEQ2368 5 SEQ1595 6 SEQ2382 7 SEQ0859 8 SEQ3112 9 SEQ1869 10 SEQ1406 11 SEQ0043 12 SEQ0363 13 SEQ0069 14 SEQ1947 15

TABLE 7 Confusion matrix of the best model for this classification Low LVEF predicted High LVEF predicted Low LVEF real 8 2 High LVEF real 1 19

Comparison Between Low LVEF (LVEF≤45) and High LVEF (LVEF>45)

In this analysis, samples were grouped into 2 groups using the threshold of 45% LVEF: low LVEF (LVEF≤45) and high LVEF (LVEF>45). The volcano plot showed the differential expression of lncRNA. 147 lncRNAs are differentially expressed and among them 15 lncRNA are differentially expressed and have a fold change>2 or <0.5 between the low LVEF (LVEF≤45) and the high LVEF (LVEF>45) groups. The p-value and the fold-change of these lncRNA are listed in the Table 8. 206 lncRNAs which have a P<0.05 and/or an individual AUC>0.7 or <0.3 are listed in Table 9.

TABLE 8 List of 15 lncRNAs which are differentially expressed and have a fold change > 2 or <0.5 between the low LVEF group (LVEF ≤ 45) and the high LVEF group (LVEF > 45) lncRNA p-value fold change lncRNA p-value fold change SEQ2114 0.03396 0.471 SEQ1167 0.01103 0.222 SEQ2512 0.04168 0.498 SEQ1719 0.04844 0.434 SEQ0372 0.02201 0.427 SEQ0917 0.00885 0.499 SEQ0821 0.03922 0.499 SEQ2295 0.02772 3.217 SEQ0664 0.00001 0.253 SEQ1692 0.00763 0.453 SEQ1239 0.02909 0.499 SEQ1707 0.00490 0.463 SEQ2709 0.04561 0.433 SEQ2477 0.02006 2.142 SEQ1385 0.03278 0.490

TABLE 9 List of 206 IncRNAs which are differentially expressed and/or have an AUC >0.7 or <0.3 between the low LVEF group (LVEF ≤ 45) and the high LVEF group (LVEF > 45) IncRNA p-value AUC SEQ0005 0.029 0.72 SEQ0022 0.046 0.62 SEQ0023 0.012 0.73 SEQ0024 0.010 0.25 SEQ0037 0.056 0.72 SEQ0043 0.074 0.23 SEQ0069 0.054 0.26 SEQ0076 0.051 0.73 SEQ0139 0.016 0.75 SEQ0141 0.039 0.29 SEQ0147 0.021 0.72 SEQ0173 0.020 0.74 SEQ0190 0.016 0.75 SEQ0213 0.123 0.72 SEQ0216 0.095 0.71 SEQ0226 0.060 0.71 SEQ0227 0.054 0.72 SEQ0276 0.052 0.29 SEQ0321 0.059 0.71 SEQ0334 0.023 0.77 SEQ0336 0.032 0.75 SEQ0348 0.158 0.70 SEQ0357 0.025 0.72 SEQ0372 0.022 0.73 SEQ0400 0.015 0.75 SEQ0440 0.022 0.75 SEQ0472 0.033 0.74 SEQ0493 0.042 0.73 SEQ0502 0.065 0.71 SEQ0544 0.019 0.75 SEQ0586 0.025 0.73 SEQ0615 0.066 0.70 SEQ0664 0.000 0.95 SEQ0670 0.032 0.74 SEQ0688 0.040 0.72 SEQ0724 0.019 0.72 SEQ0758 0.043 0.75 SEQ0778 0.524 0.73 SEQ0781 0.031 0.71 SEQ0790 0.038 0.72 SEQ0821 0.039 0.71 SEQ0838 0.027 0.73 SEQ0845 0.068 0.70 SEQ0867 0.039 0.72 SEQ0885 0.035 0.30 SEQ0886 0.041 0.71 SEQ0891 0.059 0.30 SEQ0892 0.055 0.28 SEQ0914 0.037 0.23 SEQ0915 0.018 0.76 SEQ0917 0.009 0.78 SEQ0935 0.030 0.69 SEQ0983 0.055 0.28 SEQ1066 0.019 0.75 SEQ1089 0.012 0.76 SEQ1097 0.065 0.28 SEQ1103 0.073 0.29 SEQ1109 0.041 0.70 SEQ1162 0.030 0.72 SEQ1188 0.047 0.68 SEQ1191 0.039 0.73 SEQ1204 0.062 0.72 SEQ1207 0.006 0.76 SEQ1231 0.018 0.25 SEQ1237 0.104 0.29 SEQ1251 0.011 0.76 SEQ1281 0.031 0.24 SEQ1302 0.033 0.27 SEQ1315 0.051 0.71 SEQ1321 0.069 0.72 SEQ1329 0.032 0.26 SEQ1337 0.057 0.72 SEQ1377 0.012 0.76 SEQ1385 0.033 0.75 SEQ1402 0.030 0.73 SEQ1403 0.034 0.76 SEQ1404 0.031 0.72 SEQ1406 0.011 0.77 SEQ1426 0.040 0.75 SEQ1428 0.005 0.22 SEQ1446 0.083 0.74 SEQ1454 0.063 0.70 SEQ1468 0.024 0.76 SEQ1483 0.032 0.27 SEQ1489 0.141 0.26 SEQ1499 0.078 0.30 SEQ1564 0.011 0.73 SEQ1576 0.096 0.70 SEQ1601 0.078 0.29 SEQ1667 0.063 0.71 SEQ1674 0.055 0.73 SEQ1692 0.008 0.82 SEQ1707 0.005 0.78 SEQ1719 0.048 0.71 SEQ1728 0.042 0.32 SEQ1737 0.008 0.27 SEQ1748 0.111 0.72 SEQ1767 0.036 0.29 SEQ1793 0.067 0.73 SEQ1804 0.048 0.69 SEQ1819 0.035 0.74 SEQ1820 0.048 0.26 SEQ1821 0.055 0.71 SEQ1858 0.054 0.27 SEQ1869 0.003 0.81 SEQ1873 0.071 0.71 SEQ1923 0.017 0.72 SEQ1983 0.002 0.84 SEQ2049 0.029 0.74 SEQ2074 0.022 0.24 SEQ2100 0.041 0.69 SEQ2114 0.034 0.68 SEQ2121 0.035 0.76 SEQ2126 0.031 0.27 SEQ2127 0.220 0.73 SEQ2170 0.013 0.19 SEQ2209 0.124 0.71 SEQ2216 0.033 0.72 SEQ2234 0.032 0.26 SEQ2253 0.004 0.21 SEQ2255 0.055 0.70 SEQ2260 0.060 0.27 SEQ2273 0.052 0.72 SEQ2282 0.043 0.29 SEQ2287 0.009 0.22 SEQ2288 0.024 0.15 SEQ2313 0.013 0.74 SEQ2320 0.051 0.72 SEQ2344 0.028 0.71 SEQ2362 0.031 0.76 SEQ2368 0.013 0.74 SEQ2372 0.035 0.72 SEQ2373 0.002 0.85 SEQ2377 0.009 0.77 SEQ2382 0.029 0.73 SEQ2402 0.012 0.83 SEQ2411 0.077 0.70 SEQ2420 0.043 0.73 SEQ2454 0.015 0.75 SEQ2466 0.041 0.70 SEQ2470 0.072 0.28 SEQ2471 0.039 0.76 SEQ2472 0.022 0.27 SEQ2478 0.027 0.27 SEQ2485 0.033 0.33 SEQ2502 0.061 0.71 SEQ2512 0.042 0.70 SEQ2521 0.031 0.32 SEQ2523 0.066 0.73 SEQ2558 0.160 0.72 SEQ2571 0.013 0.76 SEQ2583 0.115 0.28 SEQ2622 0.023 0.24 SEQ2625 0.027 0.72 SEQ2637 0.046 0.31 SEQ2657 0.036 0.65 SEQ2658 0.040 0.28 SEQ2677 0.022 0.75 SEQ2692 0.052 0.29 SEQ2699 0.020 0.27 SEQ2703 0.020 0.76 SEQ2712 0.091 0.30 SEQ2737 0.072 0.70 SEQ2742 0.034 0.73 SEQ2750 0.000 0.88 SEQ2791 0.045 0.28 SEQ2825 0.046 0.72 SEQ2830 0.013 0.76 SEQ2856 0.017 0.73 SEQ2875 0.019 0.26 SEQ2880 0.054 0.28 SEQ2883 0.028 0.35 SEQ2896 0.012 0.25 SEQ2912 0.102 0.72 SEQ2928 0.033 0.69 SEQ2957 0.048 0.31 SEQ2968 0.045 0.28 SEQ2982 0.002 0.19 SEQ2984 0.043 0.28 SEQ2998 0.005 0.79 SEQ3006 0.026 0.72 SEQ3010 0.016 0.23 SEQ3053 0.013 0.76 SEQ3054 0.019 0.27 SEQ3056 0.030 0.71 SEQ3061 0.023 0.71 SEQ3064 0.023 0.77 SEQ3080 0.033 0.26 SEQ3084 0.034 0.73 SEQ3096 0.044 0.31 SEQ3104 0.070 0.30 SEQ3112 0.010 0.22 SEQ3125 0.041 0.71 SEQ3128 0.041 0.32 SEQ3133 0.080 0.70 SEQ3137 0.163 0.73 SEQ3184 0.049 0.28 SEQ3187 0.038 0.30 SEQ3193 0.065 0.71 SEQ3196 0.030 0.29 SEQ3197 0.029 0.71 SEQ3200 0.015 0.26 SEQ3210 0.036 0.70 SEQ3215 0.012 0.24 SEQ3230 0.012 0.27 SEQ3231 0.016 0.75

For this classification, the 2 groups (low LVEF (LVEF≤45) and high LVEF (LVEF>45)) have the same number of samples. The variable selection was performed by using a Random Forest model. A combination of 11 pre-selected lncRNAs through a Random Forest Classifier (Table 10) is the best predictive model obtained here. The lncRNAs were selected using a random forest algorithm. This model has an area under the receiver-operating characteristic curve (AUC) of 0.996, an accuracy of 0.933, a sensitivity of 0.882, a specificity of 1, a Positive Predictive Value (PPV) of 1 and Negative Predictive Value (PNV) of 0.867. The confusion matrix is presented in Table 11.

TABLE 10 List of 11 pre-selected lncRNAs through a Random Forest Classifier for the classification low LVEF (LVEF ≤ 45) and high LVEF (LVEF > 45) lncRNA Ranking SEQ2373 1 SEQ1748 2 SEQ3112 3 SEQ1231 4 SEQ0664 5 SEQ1686 6 SEQ0791 7 SEQ2126 8 SEQ2750 9 SEQ3010 10 SEQ2241 11

TABLE 11 Confusion matrix Low LVEF predicted High LVEF predicted Low LVEF real 15 2 High LVEF real 0 13

Correlation Between LncRNA and Left Ventricular Ejection Fraction

Instead of applying a threshold to predict patients as HF or non HF, the expression level of LncRNAs can be considered as a continuous value. For this approach, spearman correlation factor is calculated to measure the correlation between LVEF value at one month and expression level of LncRNA. When a threshold of (+ or −) 0.45 for correlation factor is applied, the expression of 73 lncRNAs are positively or negatively correlated with LVEF at 1 month. Among these 73 lncRNAs, 26 have a positive correlation factor whereas 47 have a negative correlation factor (Table 12).

TABLE 12 List of 73 IncRNA with spearman correlation factor higher than 0.45 (absolute value) LncRNA Correlation SEQ0005 −0.52414 SEQ0008 −0.45621 SEQ0069 −0.56061 SEQ0173 −0.52934 SEQ0285 −0.47612 SEQ0321 −0.52163 SEQ0334 −0.49958 SEQ0352 0.60914 SEQ0398 0.607739 SEQ0544 0.46328 SEQ0566 0.461135 SEQ0586 0.510946 SEQ0664 0.547218 SEQ0688 −0.45551 SEQ0758 −0.46513 SEQ0914 −0.55591 SEQ1109 −0.5676 SEQ1144 −0.45238 SEQ1204 −0.45716 SEQ1281 0.466222 SEQ1385 −0.45266 SEQ1398 −0.50488 SEQ1406 −0.55967 SEQ1428 −0.5583 SEQ1564 −0.61193 SEQ1626 0.457149 SEQ1674 0.566205 SEQ1707 0.467787 SEQ1715 0.477576 SEQ1804 −0.48111 SEQ1858 −0.52538 SEQ1869 −0.4541 SEQ2100 0.534861 SEQ2157 −0.52703 SEQ2216 −0.53537 SEQ2253 −0.50086 SEQ2281 −0.46295 SEQ2287 −0.63378 SEQ2311 −0.58252 SEQ2368 0.510665 SEQ2373 −0.55046 SEQ2377 −0.45729 SEQ2382 −0.48369 SEQ2402 −0.51064 SEQ2454 −0.48739 SEQ2470 0.495523 SEQ2472 −0.46052 SEQ2478 −0.46735 SEQ2501 0.470795 SEQ2523 −0.51113 SEQ2545 −0.49398 SEQ2593 −0.4538 SEQ2637 0.455663 SEQ2645 −0.49274 SEQ2703 0.459314 SEQ2742 −0.45062 SEQ2746 −0.47907 SEQ2750 0.542019 SEQ2753 0.514263 SEQ2830 0.460882 SEQ2896 0.499645 SEQ2928 0.463878 SEQ2930 −0.48812 SEQ2971 0.50357 SEQ2973 0.483104 SEQ2982 −0.4529 SEQ2998 0.49442 SEQ3013 0.476852 SEQ3080 −0.48109 SEQ3128 −0.66808 SEQ3196 −0.49516 SEQ3200 0.536685 SEQ3230 −0.50558

Example 4 LncRNA Detection in Serum Samples with a Targeted lncRNA-seq (FiMICS) Protocol

Circulating lncRNAs in body fluids such as whole blood, serum or plasma are numerous and released from many different tissues. Thus, performing total RNA sequencing on peripheral samples implies to generate a high amount of data to get sufficient data on the lncRNAs of interest. To optimize cardiac lncRNA quantification in peripheral blood samples, a targeted sequencing kit is developed to specifically quantify the cardiac lncRNAs of interest. For this purpose, capture probes of 50 nucleotides specific and complementary to the sequence of lncRNAs associated to the cardiac tissue (SEQ ID NO 1 to SEQ ID NO 3238) are designed. Each probe covers region of 200 bp. Multiple probes are designed for each lncRNA over 200 bp to cover specific region. Maximum probe coverage is limited to 2000 nucleotides. Celemics technology was used to develop the assay but similar technologies using capture probes for targeting sequencing panel can be used.

Material and Methods:

Serum samples collected at discharge of patient between D3 and D5 from 30 patients with AMI from the MitoCare cohort were used for lncRNA profiling. Mitocare is a multicenter, randomized, double-blind, placebo controlled study. The study population includes AMI patients undergoing PCI, older than 18 years. The primary endpoint is the level of left ventricular ejection fraction (LVEF) less than 40% at 1 month. Demographics of the patients are presented in Table 13. Control serum samples were selected from subjects of ADDIA Chronobiological study.

TABLE 13 Demographic data for Mitocare patients used with Fi-MICS test Group 1 Group 2 Group 3 EF <40 41-50 >50 Nb 6 6 5 Age 62.8 63.8 59.9 Male 100% 83% 60% BMI 27.9 28.0 27.6 Systolic Blood 108 123.5 117.4 Pressure Diastolic Blood 70.5 70.7 66.2 Pressure Heart Rate 83.0 79.6 67.4

Sequencing libraries constructed in Example 3 from Serum RNA of 18 patients who suffered AMI, (6 who developed heart failure (HF) and 12 who did not) and 6 control subjects are used. The lncRNA capture panel called Fi-MICS kit is used to capture 3238 cardiac lncRNAs of interest, according to the manufacturer instructions. Briefly, biotinylated target capture probes, specific for the lncRNAs of interest, are hybridized to the sequencing libraries for 24 hours. So, captured lncRNA sequences are purified on T1 streptavidin coated magnetic beads. Six successive washes are performed to eliminate all libraries sequences not specific to the panel probes. Finally, captures sequenced are enriched by PCR (14 cycles) and PCR products are purified with a final AMPure XP beads wash. Captured libraries are eluted in 30 μl of nuclease-free water.

For quality control, 1 μl of each library is run on the Agilent Technologies 2100 Bioanalyzer using a DNA 1000 chip according to the manufacturer's recommendations. Absence of adapter dimers is checked and the average library size is determined by a region table. Libraries are quantified on Qubit 2.0 using Qubit dsDNA High Sensitivity assay kit (Invitrogen). Library size previously determined on the Bioanalyzer is used to calculate molar concentrations from mass concentrations. All libraries are sequenced using the Illumina NextSeq500 (2×75 bp).

Sequencing Analysis and Statistical Analysis

The read alignment and the quantification are performed as described in Example 3. The transcript counts were normalized by CPM (counts per millions). To determine differentially expressed lncRNAs, a statistical analysis is performed using a non-parametric Wilcoxon-Mann-Whitney test and a parametric T-test. A lncRNA with a p-value≤0.05 is considered as differentially expressed.

Results:

Coverage in Targeted Sequencing is Improved

The average coverage depth across all bases in the sample is the sum of the read depths of each base in each region divided by the sum of the lengths of every region. Using the Fi-MICS kit, the average coverage is improved (11 times better in average with equivalent number of reads) compared to a total RNA-seq protocol, as shown in Table 14. Among the 3238 lncRNAs present in the panel, 2432 lncRNAs passed the threshold of 10 CPM in serum samples. Detection and quantification in function of coverage depth is presented in FIG. 5. Whereas 2744 lncRNAs are measured with a coverage of at least 1× by total RNA-Seq experiment, 3162 lncRNAs are measured with a coverage of at least 1× with FiMICS panel with 10 fold less reads generated. At a coverage of at least 2×, half of the lncRNAs are excluded with total-RNA-Seq approach (1385) whereas 3041 lncRNAs are passing the threshold in FiMICS panel. Efficiency of the targeted panel is highly enhanced (FIG. 5). The FiMICS (targeted sequencing) detects more lncRNA in terms of numbers of lncRNAs and their level of expression and thus using much less total sequencing reads.

TABLE 14 Number of reads and average coverage for 18 samples in the 2 sequencing protocols Total RNA-seq protocol Targeted RNA-seq protocol Sample Total Average Total Average name reads coverage depth reads coverage depth Sample 1 35,545,396 62.01 4,113,215 135.54 Sample 2 34,427,599 70.57 5,051,804 107.11 Sample 3 27,820,331 64.19 7,664,878 100.01 Sample 4 46,070,066 87.04 5,939,425 94.2 Sample 5 37,846,232 76.60 5,251,571 96.98 Sample 6 45,285,008 51.97 8,649,560 118.7 Sample 7 63,215,798 88.00 5,342,296 99.26 Sample 8 37,467,050 67.20 6,552,391 93.25 Sample 9 65,796,180 87.51 6,602,505 129.06 Sample 10 50,693,623 48.89 5,043,709 76.41 Sample 11 64,165,816 88.80 6,586,358 83.5 Sample 12 33,302,080 54.82 6,725,419 105.28 Sample 13 29,673,123 50.11 8,178,840 123.15 Sample 14 56,386,693 76.81 5,613,486 105.63 Sample 15 75,267,997 107.00 6,789,160 124.8 Sample 16 40,789,456 66.70 5,875,488 81.59 Sample 17 54,651,503 78.11 7,038,893 85.31 Sample 18 66,866,920 78.91 5,275,438 82.16

Comparison Between Samples After Myocardial Infarction and Control Samples

First, the statistical analysis was performed by comparing 18 samples after myocardial infarction (AMI) and 6 control samples with the goal to diagnose myocardial infraction. The volcano plot showed the differential expression of lncRNA. 20 lncRNAs are differentially expressed between the samples AMI and the control samples. The p-value and the fold-change of these lncRNA are listed in the Table 15.

TABLE 15 List of 20 lncRNAs which are differentially expressed between samples AMI and control samples lncRNA p-value Fold change SEQ0097 1.35E−05 0.446 SEQ2114 0.00194062 0.477 SEQ0534 0.02513143 0.354 SEQ1404 0.0128132 0.486 SEQ0311 0.00046383 0.217 SEQ1262 0.01381743 0.412 SEQ0990 0.00060722 0.182 SEQ1300 0.04098375 0.364 SEQ0978 0.00358642 0.498 SEQ0215 0.00013071 0.369 SEQ0288 0.04991173 0.392 SEQ1418 0.00010606 0.450 SEQ2070 0.00078855 0.457 SEQ0309 0.00322822 0.141 SEQ0597 0.0182368 0.401 SEQ1875 0.0343985 0.457 SEQ1984 0.0108457 0.479 SEQ0538 3.89E−05 0.386 SEQ1871 0.00021278 0.360

For this classification, a combination of 14 pre-selected lncRNA through a Random Forest Classifier (Table 16) is the best predictive model obtained here. The lncRNAs were selected using a random forest algorithm. This model has an area under the receiver-operating characteristic curve (AUC) of 0.971, an accuracy of 0.870, a sensitivity of 0.941, a specificity of 0.667, a Positive Predictive Value (PPV) of 0.889 and Negative Predictive Value (PNV) of 0.800. The confusion matrix is presented in Table 17.

TABLE 16 List of 14 pre-selected lncRNAs through a Random Forest Classifier for the classification between the samples AMI and the control samples lncRNA rank SEQ2150 1 SEQ1534 2 SEQ0311 3 SEQ2952 4 SEQ2838 5 SEQ1437 6 SEQ1297 7 SEQ1059 8 SEQ1465 9 SEQ2826 10 SEQ0180 11 SEQ0538 12 SEQ0258 13 SEQ2273 14

TABLE 17 Confusion matrix of the Random Forest model Predicted AMI Predicted Control Real Control 4 2 True AMI 1 16

Comparison Between Low LVEF (LVEF≤40) and High LVEF (LVEF>40)

In this analysis, the 18 samples AMI were grouped into 2 groups based on the 1-month LVEF: low LVEF (LVEF≤40) and high LVEF (LVEF>40). The volcano plot showed the differential expression of lncRNA. 95 lncRNAs are differentially expressed and among them, 6 lncRNAs are differentially expressed with a fold change>2 or <0.5 between the samples with low LVEF and the samples with high LVEF. The p-value and the fold-change and individual AUC of these 6 lncRNAs are listed in the Table 18 and 353 lncRNAs which have a P<0.05 and/or an individual AUC>0.7 or <0.3 are listed in Table 19.

TABLE 18 List of 6 lncRNAs which are differentially expressed and have a fold change > 2 or <0.5 between the low LVEF group (LVEF ≤ 40) and the high LVEF group (LVEF > 40) lncRNA p-value Fold change Individual AUC SEQ0631 0.022 2.497 0.848 SEQ0758 0.030 0.354 0.242 SEQ0789 0.030 0.388 0.258 SEQ1399 0.021 0.163 0.242 SEQ2914 0.012 2.493 0.985 SEQ2924 0.147 2.232 0.727

TABLE 19 List of 353 IncRNAs which are differentially expressed and/or have an AUC >0.7 or <0.3 between the low LVEF group (LVEF ≤ 40) and the high LVEF group (LVEF > 40) IncRNA p-value AUC SEQ0002 0.006 0.939 SEQ0006 0.965 0.712 SEQ0007 0.199 0.712 SEQ0008 0.224 0.288 SEQ0018 0.5 0.258 SEQ0019 0.027 0.182 SEQ0023 0.127 0.742 SEQ0041 0.091 0.258 SEQ0042 0.151 0.242 SEQ0048 0.145 0.288 SEQ0057 0.163 0.712 SEQ0060 0.192 0.288 SEQ0094 0.264 0.773 SEQ0106 0.168 0.273 SEQ0117 0.097 0.727 SEQ0120 0.642 0.288 SEQ0134 0.075 0.212 SEQ0149 0.448 0.712 SEQ0151 0.011 0.182 SEQ0155 0.023 0.833 SEQ0190 0.05 0.242 SEQ0191 0.064 0.818 SEQ0205 0.047 0.212 SEQ0208 0.051 0.197 SEQ0222 0.018 0.833 SEQ0228 0.171 0.712 SEQ0236 0.06 0.788 SEQ0239 0.121 0.712 SEQ0241 0.097 0.288 SEQ0242 0.462 0.727 SEQ0285 0.149 0.758 SEQ0295 0.076 0.273 SEQ0308 0.12 0.273 SEQ0312 0.075 0.212 SEQ0334 0.021 0.864 SEQ0345 0.107 0.758 SEQ0350 0.017 0.152 SEQ0354 0.346 0.727 SEQ0358 0.161 0.288 SEQ0362 0.25 0.273 SEQ0366 0.095 0.758 SEQ0371 0.349 0.258 SEQ0380 0.141 0.727 SEQ0384 0.026 0.803 SEQ0394 0.029 0.152 SEQ0412 0.342 0.227 SEQ0434 0.179 0.712 SEQ0441 0.05 0.197 SEQ0443 0.211 0.712 SEQ0445 0.446 0.288 SEQ0460 0.046 0.227 SEQ0468 0.059 0.727 SEQ0469 0.09 0.288 SEQ0487 0.091 0.212 SEQ0502 0.106 0.758 SEQ0542 0.068 0.727 SEQ0547 0.016 0.803 SEQ0551 0.196 0.742 SEQ0552 0.042 0.833 SEQ0561 0.192 0.712 SEQ0581 0.057 0.758 SEQ0597 0.108 0.742 SEQ0601 0.075 0.803 SEQ0604 0.284 0.258 SEQ0612 0.071 0.288 SEQ0621 0.21 0.742 SEQ0629 0.176 0.758 SEQ0631 0.022 0.848 SEQ0659 0.052 0.848 SEQ0661 0.157 0.742 SEQ0670 0.053 0.742 SEQ0677 0.035 0.788 SEQ0680 0.045 0.227 SEQ0681 0.047 0.773 SEQ0701 0.159 0.212 SEQ0702 0.365 0.712 SEQ0724 0.058 0.742 SEQ0726 0.515 0.712 SEQ0729 0.017 0.864 SEQ0730 0.076 0.818 SEQ0732 0.098 0.758 SEQ0751 0.03 0.212 SEQ0758 0.03 0.242 SEQ0766 0.033 0.803 SEQ0779 0.36 0.742 SEQ0789 0.03 0.258 SEQ0821 0.004 0.864 SEQ0823 0.117 0.273 SEQ0829 0.143 0.227 SEQ0841 0.063 0.773 SEQ0844 0.021 0.136 SEQ0847 0.107 0.288 SEQ0868 0.228 0.242 SEQ0884 0.322 0.288 SEQ0891 0.044 0.742 SEQ0915 0.077 0.758 SEQ0926 0.285 0.288 SEQ0937 0.075 0.727 SEQ0938 0.271 0.742 SEQ0946 0.008 0.833 SEQ0956 0.012 0.879 SEQ0958 0.027 0.818 SEQ0960 0.036 0.788 SEQ0981 0.07 0.288 SEQ0986 0.044 0.788 SEQ1005 0.178 0.712 SEQ1052 0.221 0.727 SEQ1065 0.045 0.212 SEQ1075 0.025 0.197 SEQ1076 0.275 0.288 SEQ1089 0.002 0.97 SEQ1093 0.037 0.197 SEQ1109 0.114 0.788 SEQ1111 0.139 0.288 SEQ1146 0.039 0.182 SEQ1156 0.28 0.742 SEQ1162 0.019 0.803 SEQ1164 0.181 0.273 SEQ1179 0.078 0.197 SEQ1186 0.135 0.273 SEQ1191 0.064 0.242 SEQ1204 0.012 0.848 SEQ1207 0.047 0.864 SEQ1217 0.13 0.742 SEQ1232 0.086 0.773 SEQ1252 0.208 0.273 SEQ1273 0.016 0.182 SEQ1288 0.021 0.197 SEQ1326 0.056 0.258 SEQ1333 0.199 0.712 SEQ1338 0.097 0.288 SEQ1350 0.162 0.242 SEQ1354 0.059 0.803 SEQ1399 0.021 0.242 SEQ1403 0.063 0.788 SEQ1405 0.17 0.727 SEQ1412 0.097 0.712 SEQ1422 0.04 0.758 SEQ1433 0.056 0.258 SEQ1439 0.029 0.152 SEQ1449 0.073 0.227 SEQ1459 0.125 0.242 SEQ1465 0.182 0.288 SEQ1467 0.067 0.742 SEQ1475 0.034 0.242 SEQ1476 0.022 0.833 SEQ1484 0.124 0.288 SEQ1485 0.143 0.727 SEQ1515 0.014 0.136 SEQ1516 0.076 0.818 SEQ1527 0.185 0.273 SEQ1534 0.038 0.212 SEQ1535 0.284 0.712 SEQ1556 0.133 0.727 SEQ1573 0.045 0.258 SEQ1578 0.197 0.742 SEQ1580 0.229 0.712 SEQ1598 0.146 0.712 SEQ1624 0.048 0.227 SEQ1635 0.089 0.758 SEQ1660 0.014 0.864 SEQ1661 0.038 0.258 SEQ1678 0.075 0.258 SEQ1696 0.231 0.288 SEQ1710 0.056 0.742 SEQ1722 0.091 0.864 SEQ1740 0.162 0.712 SEQ1744 0.021 0.167 SEQ1754 0.453 0.727 SEQ1760 0.086 0.727 SEQ1773 0.146 0.288 SEQ1806 0.168 0.258 SEQ1816 0.06 0.833 SEQ1818 0.106 0.288 SEQ1833 0.14 0.273 SEQ1852 0.008 0.864 SEQ1853 0.069 0.227 SEQ1854 0.164 0.773 SEQ1860 0.19 0.727 SEQ1862 0.107 0.258 SEQ1871 0.096 0.288 SEQ1872 0.142 0.712 SEQ1880 0.377 0.712 SEQ1896 0.083 0.227 SEQ1903 0.105 0.227 SEQ1908 0.066 0.758 SEQ1912 0.049 0.258 SEQ1937 0.098 0.773 SEQ1939 0.139 0.197 SEQ1959 0.012 0.212 SEQ1962 0.094 0.258 SEQ1992 0.049 0.227 SEQ1995 0.06 0.773 SEQ2000 0.06 0.197 SEQ2021 0.037 0.212 SEQ2022 0.27 0.258 SEQ2050 0.117 0.273 SEQ2084 0.104 0.788 SEQ2086 0.065 0.242 SEQ2091 0.214 0.712 SEQ2109 0.22 0.242 SEQ2141 0.128 0.242 SEQ2149 0.071 0.227 SEQ2151 0.064 0.242 SEQ2161 0.051 0.273 SEQ2170 0.099 0.227 SEQ2172 0.023 0.773 SEQ2174 0.01 0.848 SEQ2192 0.013 0.864 SEQ2198 0.027 0.803 SEQ2205 0.047 0.758 SEQ2207 0.088 0.197 SEQ2218 0.078 0.788 SEQ2220 0.105 0.758 SEQ2221 0.105 0.788 SEQ2226 0.214 0.712 SEQ2227 0.058 0.258 SEQ2235 0.032 0.167 SEQ2238 0.024 0.197 SEQ2244 0.102 0.742 SEQ2273 0.098 0.773 SEQ2285 0.107 0.242 SEQ2286 0.16 0.712 SEQ2294 0.079 0.803 SEQ2311 0.388 0.273 SEQ2318 0.114 0.758 SEQ2325 0.482 0.288 SEQ2327 0.097 0.727 SEQ2338 0.012 0.818 SEQ2341 0.086 0.242 SEQ2345 0.102 0.227 SEQ2364 0.149 0.742 SEQ2368 0.045 0.742 SEQ2371 0.144 0.258 SEQ2375 0.01 0.121 SEQ2379 0.029 0.773 SEQ2395 0.113 0.773 SEQ2406 0.018 0.182 SEQ2407 0.27 0.773 SEQ2411 0.02 0.864 SEQ2422 0.138 0.742 SEQ2425 0.15 0.712 SEQ2429 0.049 0.212 SEQ2436 0.11 0.758 SEQ2440 0.238 0.258 SEQ2441 0.067 0.242 SEQ2451 0.205 0.712 SEQ2454 0.054 0.758 SEQ2475 0.045 0.197 SEQ2497 0.109 0.712 SEQ2513 0.189 0.712 SEQ2517 0.189 0.758 SEQ2520 0.176 0.727 SEQ2529 0.256 0.273 SEQ2544 0.259 0.742 SEQ2546 0.055 0.258 SEQ2553 0.196 0.242 SEQ2562 0.099 0.712 SEQ2572 0.227 0.727 SEQ2584 0.206 0.288 SEQ2611 0.112 0.288 SEQ2613 0.105 0.758 SEQ2621 0.152 0.727 SEQ2627 0.068 0.788 SEQ2629 0.093 0.712 SEQ2639 0.131 0.288 SEQ2640 0.08 0.727 SEQ2641 0.379 0.742 SEQ2656 0.085 0.712 SEQ2676 0.03 0.864 SEQ2677 0.082 0.212 SEQ2680 0.161 0.727 SEQ2681 0.07 0.788 SEQ2683 0.053 0.818 SEQ2684 0.076 0.197 SEQ2692 0.047 0.242 SEQ2713 0.052 0.803 SEQ2735 0.261 0.712 SEQ2737 0.035 0.848 SEQ2754 0.133 0.212 SEQ2760 0.135 0.273 SEQ2767 0.156 0.727 SEQ2768 0.14 0.758 SEQ2784 0.09 0.742 SEQ2788 0.15 0.288 SEQ2789 0.426 0.727 SEQ2796 0.162 0.773 SEQ2806 0.058 0.773 SEQ2819 0.111 0.727 SEQ2827 0.024 0.894 SEQ2834 0.098 0.288 SEQ2841 0.014 0.818 SEQ2856 0.13 0.273 SEQ2857 0.135 0.742 SEQ2870 0.035 0.212 SEQ2881 0.014 0.818 SEQ2903 0.19 0.712 SEQ2911 0.177 0.742 SEQ2914 0.012 0.985 SEQ2917 0.226 0.712 SEQ2924 0.147 0.727 SEQ2939 0.06 0.258 SEQ2945 0.727 0.727 SEQ2955 0.089 0.288 SEQ2958 0.071 0.758 SEQ2959 0.34 0.879 SEQ2961 0.009 0.121 SEQ2963 0.114 0.758 SEQ2967 0.042 0.227 SEQ2969 0.22 0.727 SEQ2973 0.17 0.773 SEQ2982 0.069 0.818 SEQ2995 0.063 0.273 SEQ3001 0.088 0.727 SEQ3007 0.217 0.712 SEQ3013 0.059 0.758 SEQ3015 0.147 0.727 SEQ3029 0.03 0.212 SEQ3035 0.004 0.136 SEQ3036 0.071 0.818 SEQ3052 0.064 0.773 SEQ3053 0.002 0.909 SEQ3058 0.037 0.803 SEQ3060 0.371 0.712 SEQ3064 0.048 0.758 SEQ3065 0.16 0.742 SEQ3069 0.328 0.258 SEQ3090 0.046 0.773 SEQ3091 0.161 0.712 SEQ3098 0.094 0.212 SEQ3101 0.102 0.833 SEQ3107 0.221 0.258 SEQ3124 0.008 0.864 SEQ3130 0.134 0.742 SEQ3134 0.158 0.727 SEQ3142 0.111 0.242 SEQ3146 0.114 0.712 SEQ3147 0.237 0.273 SEQ3148 0.33 0.758 SEQ3169 0.138 0.742 SEQ3172 0.033 0.758 SEQ3176 0.037 0.879 SEQ3183 0.006 0.909 SEQ3190 0.085 0.788 SEQ3195 0.186 0.273 SEQ3196 0.036 0.773 SEQ3197 0.119 0.758 SEQ3199 0.081 0.788 SEQ3208 0.015 0.197 SEQ3209 0.133 0.258 SEQ3213 0.027 0.152 SEQ3222 0.051 0.197 SEQ3236 0.293 0.712

Comparison Between Low LVEF (LVEF≤45) and High LVEF (LVEF>45)

In this analysis, the 18 samples AMI were grouped into 2 groups using the threshold of 45% LVEF: low LVEF (LVEF≤45) and high LVEF (LVEF>45). The volcano plot showed the differential expression of lncRNA. 80 lncRNA are differentially expressed and among them, 1 lncRNA has a fold change>2 or <0.5, which is shown in Table 20. 467 lncRNAs which have a P<0.05 and/or an individual AUC>0.7 or <0.3 are listed in Table 21.

TABLE 20 List of 1 lncRNA which is differentially expressed with a fold change > 2 or <0.5 between the low LVEF group (LVEF ≤ 45) and the high LVEF group (LVEF > 45) lncRNA p-value Fold change AUC SEQ2924 0.034 2.526 0.829

TABLE 21 List of 467 IncRNAs which are differentially expressed and/or have an AUC >0.7 or <0.3 between the low LVEF group (LVEF ≤ 45) and the high LVEF group (LVEF > 45) IncRNA p-value AUC SEQ0008 0.186 0.286 SEQ0023 0.152 0.743 SEQ0024 0.151 0.3 SEQ0063 0.014 0.843 SEQ0067 0.09 0.757 SEQ0068 0.105 0.229 SEQ0071 0.106 0.2 SEQ0076 0.18 0.729 SEQ0092 0.103 0.729 SEQ0095 0.092 0.214 SEQ0104 0.286 0.3 SEQ0105 0.031 0.2 SEQ0106 0.006 0.1 SEQ0107 0.143 0.729 SEQ0108 0.118 0.729 SEQ0112 0.201 0.3 SEQ0113 0.146 0.3 SEQ0117 0.134 0.743 SEQ0127 0.015 0.843 SEQ0130 0.07 0.757 SEQ0134 0.047 0.186 SEQ0136 0.234 0.714 SEQ0139 0.089 0.771 SEQ0141 0.007 0.143 SEQ0155 0.065 0.743 SEQ0161 0.162 0.7 SEQ0162 0.191 0.3 SEQ0167 0.142 0.729 SEQ0170 0.151 0.257 SEQ0193 0.129 0.271 SEQ0194 0.029 0.2 SEQ0200 0.186 0.3 SEQ0208 0.647 0.3 SEQ0215 0.202 0.743 SEQ0217 0.099 0.3 SEQ0219 0.149 0.7 SEQ0236 0.111 0.771 SEQ0239 0.011 0.771 SEQ0242 0.184 0.757 SEQ0267 0.146 0.286 SEQ0273 0.14 0.757 SEQ0299 0.122 0.257 SEQ0309 0.383 0.729 SEQ0317 0.082 0.214 SEQ0331 0.2 0.286 SEQ0334 0.155 0.757 SEQ0343 0.119 0.743 SEQ0359 0.081 0.257 SEQ0373 0.209 0.714 SEQ0393 0.175 0.271 SEQ0394 0.041 0.157 SEQ0395 0.096 0.729 SEQ0398 0.32 0.714 SEQ0405 0.168 0.286 SEQ0412 0.522 0.229 SEQ0425 0.284 0.714 SEQ0426 0.119 0.7 SEQ0427 0.128 0.757 SEQ0434 0.381 0.7 SEQ0440 0.15 0.714 SEQ0441 0.122 0.243 SEQ0467 0.201 0.7 SEQ0474 0.252 0.757 SEQ0479 0.073 0.214 SEQ0482 0.231 0.714 SEQ0490 0.13 0.714 SEQ0493 0.142 0.714 SEQ0494 0.095 0.743 SEQ0501 0.093 0.271 SEQ0502 0.178 0.7 SEQ0510 0.108 0.3 SEQ0515 0.085 0.229 SEQ0534 0.43 0.743 SEQ0536 0.074 0.743 SEQ0538 0.259 0.7 SEQ0540 0.038 0.2 SEQ0542 0.021 0.857 SEQ0547 0.12 0.729 SEQ0549 0.104 0.743 SEQ0550 0.137 0.743 SEQ0552 0.151 0.743 SEQ0571 0.415 0.271 SEQ0574 0.168 0.3 SEQ0581 0.081 0.729 SEQ0596 0.208 0.229 SEQ0598 0.352 0.3 SEQ0603 0.238 0.286 SEQ0615 0.231 0.257 SEQ0617 0.174 0.714 SEQ0620 0.06 0.257 SEQ0635 0.089 0.214 SEQ0636 0.148 0.743 SEQ0659 0.005 0.914 SEQ0677 0.081 0.757 SEQ0698 0.048 0.771 SEQ0702 0.074 0.757 SEQ0707 0.092 0.757 SEQ0709 0.137 0.286 SEQ0716 0.017 0.186 SEQ0724 0.048 0.814 SEQ0731 0.108 0.2 SEQ0748 0.11 0.286 SEQ0750 0.009 0.143 SEQ0751 0.102 0.2 SEQ0766 0.16 0.714 SEQ0772 0.134 0.286 SEQ0779 0.716 0.714 SEQ0805 0.504 0.714 SEQ0806 0.16 0.3 SEQ0833 0.067 0.214 SEQ0839 0.178 0.714 SEQ0851 0.103 0.743 SEQ0852 0.122 0.243 SEQ0862 0.023 0.843 SEQ0864 0.174 0.257 SEQ0866 0.095 0.7 SEQ0874 0.152 0.7 SEQ0877 0.05 0.757 SEQ0892 0.061 0.171 SEQ0897 0.074 0.257 SEQ0906 0.157 0.243 SEQ0907 0.227 0.7 SEQ0933 0.122 0.229 SEQ0937 0.023 0.843 SEQ0939 0.177 0.714 SEQ0940 0.105 0.743 SEQ0946 0.083 0.743 SEQ0956 0.07 0.786 SEQ0958 0.066 0.771 SEQ0966 0.031 0.786 SEQ0986 0.029 0.814 SEQ0993 0.102 0.729 SEQ1007 0.138 0.286 SEQ1016 0.064 0.229 SEQ1025 0.023 0.214 SEQ1028 0.042 0.729 SEQ1034 0.077 0.714 SEQ1036 0.052 0.186 SEQ1053 0.044 0.229 SEQ1055 0.127 0.729 SEQ1056 0.151 0.7 SEQ1057 0.191 0.257 SEQ1080 0.139 0.743 SEQ1086 0.045 0.786 SEQ1088 0.075 0.771 SEQ1089 0.184 0.786 SEQ1093 0.129 0.271 SEQ1099 0.169 0.3 SEQ1106 0.199 0.7 SEQ1109 0.141 0.771 SEQ1111 0.48 0.3 SEQ1115 0.347 0.743 SEQ1116 0.1 0.771 SEQ1121 0.268 0.3 SEQ1129 0.108 0.257 SEQ1136 0.069 0.214 SEQ1146 0.139 0.286 SEQ1164 0.136 0.271 SEQ1182 0.126 0.743 SEQ1184 0.015 0.814 SEQ1189 0.097 0.757 SEQ1192 0.115 0.3 SEQ1204 0.19 0.7 SEQ1207 0.016 0.829 SEQ1213 0.008 0.086 SEQ1222 0.068 0.214 SEQ1237 0.059 0.186 SEQ1241 0.22 0.3 SEQ1242 0.347 0.257 SEQ1268 0.06 0.757 SEQ1270 0.121 0.257 SEQ1273 0.147 0.257 SEQ1291 0.067 0.257 SEQ1300 0.097 0.8 SEQ1304 0.216 0.714 SEQ1310 0.022 0.157 SEQ1321 0.081 0.257 SEQ1328 0.129 0.3 SEQ1336 0.047 0.743 SEQ1343 0.132 0.714 SEQ1345 0.188 0.286 SEQ1350 0.118 0.3 SEQ1354 0.181 0.714 SEQ1369 0.141 0.271 SEQ1378 0.28 0.286 SEQ1379 0.181 0.743 SEQ1381 0.757 0.286 SEQ1384 0.095 0.271 SEQ1398 0.468 0.3 SEQ1403 0.096 0.757 SEQ1406 0.108 0.271 SEQ1409 0.218 0.229 SEQ1411 0.091 0.757 SEQ1426 0.165 0.714 SEQ1433 0.006 0.129 SEQ1439 0.056 0.229 SEQ1440 0.198 0.3 SEQ1445 0.229 0.7 SEQ1458 0.149 0.771 SEQ1474 0.092 0.257 SEQ1478 0.27 0.3 SEQ1490 0.223 0.3 SEQ1491 0.195 0.3 SEQ1493 0.042 0.2 SEQ1495 0.185 0.3 SEQ1504 0.211 0.271 SEQ1508 0.115 0.157 SEQ1515 0.251 0.257 SEQ1516 0.21 0.729 SEQ1536 0.066 0.229 SEQ1537 0.127 0.7 SEQ1539 0.168 0.729 SEQ1548 0.183 0.3 SEQ1558 0.079 0.229 SEQ1570 0.014 0.171 SEQ1573 0.107 0.271 SEQ1576 0.044 0.786 SEQ1587 0.009 0.9 SEQ1591 0.192 0.714 SEQ1592 0.24 0.743 SEQ1593 0.032 0.814 SEQ1594 0.147 0.286 SEQ1599 0.101 0.729 SEQ1609 0.059 0.186 SEQ1623 0.153 0.271 SEQ1638 0.1 0.3 SEQ1647 0.181 0.7 SEQ1649 0.054 0.229 SEQ1656 0.102 0.271 SEQ1660 0.067 0.786 SEQ1671 0.421 0.257 SEQ1678 0.148 0.286 SEQ1691 0.223 0.7 SEQ1692 0.207 0.7 SEQ1708 0.298 0.3 SEQ1722 0.078 0.771 SEQ1744 0.204 0.271 SEQ1754 0.13 0.714 SEQ1755 0.16 0.729 SEQ1758 0.103 0.757 SEQ1771 0.057 0.2 SEQ1777 0.016 0.871 SEQ1788 0.093 0.729 SEQ1815 0.108 0.743 SEQ1833 0.122 0.229 SEQ1834 0.182 0.729 SEQ1842 0.099 0.743 SEQ1852 0.003 0.914 SEQ1854 0.032 0.857 SEQ1882 0.06 0.143 SEQ1887 0.567 0.3 SEQ1888 0.184 0.729 SEQ1903 0.126 0.186 SEQ1913 0.165 0.286 SEQ1944 0.039 0.786 SEQ1947 0.1 0.757 SEQ1951 0.196 0.243 SEQ1962 0.071 0.229 SEQ1972 0.129 0.757 SEQ1976 0.193 0.7 SEQ1995 0.174 0.743 SEQ2003 0.106 0.729 SEQ2021 0.06 0.214 SEQ2024 0.097 0.729 SEQ2031 0.032 0.186 SEQ2068 0.147 0.3 SEQ2079 0.261 0.3 SEQ2082 0.052 0.771 SEQ2085 0.141 0.743 SEQ2086 0.101 0.286 SEQ2109 0.12 0.271 SEQ2113 0.125 0.2 SEQ2114 0.057 0.743 SEQ2131 0.005 0.1 SEQ2138 0.209 0.3 SEQ2157 0.043 0.743 SEQ2159 0.228 0.7 SEQ2171 0.2 0.7 SEQ2176 0.036 0.771 SEQ2177 0.335 0.714 SEQ2192 0.285 0.729 SEQ2202 0.173 0.3 SEQ2204 0.122 0.243 SEQ2205 0.154 0.743 SEQ2217 0.195 0.286 SEQ2226 0.12 0.729 SEQ2227 0.024 0.157 SEQ2234 0.16 0.257 SEQ2235 0.065 0.214 SEQ2244 0.63 0.7 SEQ2252 0.006 0.9 SEQ2264 0.206 0.3 SEQ2268 0.013 0.086 SEQ2270 0.146 0.257 SEQ2273 0.026 0.857 SEQ2279 0.121 0.3 SEQ2281 0.108 0.714 SEQ2289 0.145 0.7 SEQ2294 0.082 0.729 SEQ2297 0.619 0.714 SEQ2305 0.082 0.757 SEQ2309 0.117 0.757 SEQ2318 0.066 0.714 SEQ2319 0.264 0.3 SEQ2321 0.021 0.771 SEQ2326 0.126 0.743 SEQ2334 0.285 0.257 SEQ2336 0.085 0.757 SEQ2339 0.15 0.729 SEQ2347 0.043 0.743 SEQ2355 0.207 0.3 SEQ2375 0.349 0.3 SEQ2379 0.036 0.857 SEQ2382 0.072 0.229 SEQ2386 0.172 0.257 SEQ2388 0.289 0.271 SEQ2389 0.015 0.171 SEQ2392 0.189 0.243 SEQ2393 0.124 0.257 SEQ2395 0.068 0.714 SEQ2402 0.438 0.714 SEQ2405 0.001 0.929 SEQ2406 0.049 0.186 SEQ2408 0.22 0.257 SEQ2409 0.045 0.829 SEQ2410 0.102 0.257 SEQ2420 0.08 0.743 SEQ2427 0.038 0.8 SEQ2429 0.082 0.186 SEQ2433 0.105 0.257 SEQ2437 0.058 0.757 SEQ2440 0.157 0.257 SEQ2450 0.101 0.229 SEQ2454 0.058 0.771 SEQ2459 0.03 0.8 SEQ2472 0.2 0.271 SEQ2475 0.303 0.286 SEQ2487 0.115 0.786 SEQ2492 0.147 0.3 SEQ2497 0.149 0.729 SEQ2501 0.138 0.743 SEQ2503 0.122 0.7 SEQ2511 0.314 0.286 SEQ2513 0.048 0.857 SEQ2518 0.075 0.243 SEQ2521 0.153 0.286 SEQ2529 0.099 0.271 SEQ2532 0.164 0.714 SEQ2533 0.02 0.157 SEQ2552 0.107 0.214 SEQ2555 0.504 0.3 SEQ2561 0.214 0.3 SEQ2576 0.01 0.114 SEQ2599 0.18 0.271 SEQ2602 0.048 0.229 SEQ2606 0.021 0.857 SEQ2632 0.186 0.257 SEQ2637 0.007 0.857 SEQ2647 0.171 0.286 SEQ2648 0.161 0.257 SEQ2660 0.111 0.286 SEQ2675 0.306 0.286 SEQ2676 0.101 0.7 SEQ2690 0.231 0.271 SEQ2692 0.153 0.271 SEQ2695 0.105 0.743 SEQ2696 0.33 0.3 SEQ2701 0.111 0.3 SEQ2706 0.136 0.286 SEQ2712 0.213 0.286 SEQ2726 0.051 0.229 SEQ2727 0.399 0.3 SEQ2729 0.129 0.243 SEQ2735 0.241 0.729 SEQ2740 0.19 0.271 SEQ2741 0.714 0.3 SEQ2745 0.086 0.729 SEQ2751 0.102 0.2 SEQ2760 0.017 0.186 SEQ2765 0.208 0.7 SEQ2768 0.333 0.714 SEQ2777 0.066 0.243 SEQ2785 0.029 0.2 SEQ2788 0.161 0.257 SEQ2795 0.201 0.3 SEQ2796 0.276 0.7 SEQ2805 0.054 0.243 SEQ2815 0.196 0.3 SEQ2827 0.061 0.771 SEQ2829 0.076 0.814 SEQ2834 0.216 0.257 SEQ2852 0.145 0.286 SEQ2857 0.034 0.843 SEQ2859 0.111 0.3 SEQ2860 0.075 0.214 SEQ2891 0.18 0.286 SEQ2916 0.101 0.257 SEQ2920 0.084 0.229 SEQ2922 0.126 0.186 SEQ2924 0.034 0.829 SEQ2928 0.268 0.7 SEQ2930 0.247 0.257 SEQ2933 0.081 0.229 SEQ2956 0.113 0.271 SEQ2957 0.091 0.286 SEQ2959 0.885 0.7 SEQ2961 0.014 0.186 SEQ2963 0.128 0.714 SEQ2967 0.134 0.257 SEQ2972 0.378 0.743 SEQ2974 0.169 0.743 SEQ2977 0.043 0.129 SEQ2978 0.261 0.271 SEQ2986 0.062 0.229 SEQ2988 0.141 0.257 SEQ2993 0.026 0.171 SEQ2995 0.152 0.286 SEQ2996 0.197 0.3 SEQ2997 0.054 0.243 SEQ2998 0.089 0.243 SEQ3009 0.224 0.3 SEQ3017 0.168 0.271 SEQ3027 0.389 0.3 SEQ3030 0.165 0.271 SEQ3040 0.036 0.8 SEQ3042 0.214 0.186 SEQ3054 0.188 0.243 SEQ3058 0.091 0.757 SEQ3064 0.171 0.714 SEQ3067 0.148 0.286 SEQ3069 0.291 0.3 SEQ3077 0.212 0.3 SEQ3078 0.057 0.786 SEQ3079 0.031 0.186 SEQ3083 0.171 0.286 SEQ3092 0.283 0.243 SEQ3102 0.209 0.3 SEQ3111 0.303 0.286 SEQ3119 0.042 0.229 SEQ3124 0.04 0.829 SEQ3126 0.158 0.714 SEQ3129 0.152 0.271 SEQ3140 0.185 0.271 SEQ3141 0.036 0.214 SEQ3142 0.015 0.157 SEQ3144 0.145 0.243 SEQ3147 0.037 0.171 SEQ3148 0.19 0.714 SEQ3154 0.302 0.714 SEQ3156 0.09 0.257 SEQ3157 0.092 0.243 SEQ3169 0.005 0.914 SEQ3170 0.428 0.286 SEQ3176 0.032 0.771 SEQ3178 0.017 0.2 SEQ3179 0.235 0.3 SEQ3182 0.064 0.786 SEQ3183 0.059 0.743 SEQ3186 0.092 0.2 SEQ3207 0.123 0.257 SEQ3208 0.138 0.3 SEQ3209 0.11 0.257 SEQ3210 0.055 0.757 SEQ3213 0.052 0.157 SEQ3221 0.207 0.3 SEQ3222 0.092 0.229 SEQ3228 0.265 0.3

Correlation Between LncRNA and Left Ventricular Ejection Fraction

LncRNAs expression level can be considered as a continuous value. Spearman correlation factor is calculated to measure the correlation between LVEF value at one month and expression level. When a threshold of (+ or −) 0.45 for correlation factor is applied, the expression of 159 lncRNAs is positively or negatively correlated with prediction of LVEF at 1 month. Among these 159 lncRNAs, 94 have a positive correlation factor whereas 65 have a negative correlation factor (Table 22).

TABLE 22 List of 159 IncRNAs with spearman correlation factor higher than 0.45 (absolute value) LncRNA correlation SEQ0002 −0.522 SEQ0005 −0.477 SEQ0008 0.565 SEQ0068 0.461 SEQ0104 0.454 SEQ0108 −0.581 SEQ0111 0.67 SEQ0134 0.729 SEQ0139 −0.489 SEQ0155 −0.511 SEQ0168 0.522 SEQ0210 −0.458 SEQ0219 −0.476 SEQ0246 0.523 SEQ0292 0.585 SEQ0343 −0.47 SEQ0394 0.497 SEQ0443 −0.573 SEQ0462 0.452 SEQ0487 0.456 SEQ0510 0.504 SEQ0536 −0.481 SEQ0596 0.544 SEQ0624 0.493 SEQ0635 0.503 SEQ0639 0.482 SEQ0659 −0.486 SEQ0677 −0.519 SEQ0681 −0.547 SEQ0698 −0.666 SEQ0701 0.455 SEQ0716 0.529 SEQ0731 0.518 SEQ0766 −0.476 SEQ0772 0.524 SEQ0833 0.471 SEQ0841 −0.527 SEQ0884 0.472 SEQ0914 0.454 SEQ0946 −0.451 SEQ0958 −0.482 SEQ0966 −0.545 SEQ0980 0.456 SEQ0986 −0.651 SEQ1055 −0.455 SEQ1057 0.585 SEQ1065 0.667 SEQ1075 0.474 SEQ1093 0.461 SEQ1207 −0.591 SEQ1208 0.543 SEQ1213 0.541 SEQ1222 0.466 SEQ1270 0.516 SEQ1299 −0.479 SEQ1343 −0.593 SEQ1354 −0.47 SEQ1403 −0.463 SEQ1412 −0.524 SEQ1433 0.564 SEQ1440 0.575 SEQ1465 0.632 SEQ1477 0.553 SEQ1508 0.667 SEQ1558 0.57 SEQ1560 0.567 SEQ1573 0.525 SEQ1587 −0.465 SEQ1594 0.499 SEQ1598 −0.496 SEQ1660 −0.47 SEQ1678 0.507 SEQ1682 0.451 SEQ1687 −0.49 SEQ1698 −0.53 SEQ1723 −0.581 SEQ1740 −0.533 SEQ1794 0.517 SEQ1852 −0.541 SEQ1854 −0.534 SEQ1899 0.564 SEQ1935 0.55 SEQ1962 0.473 SEQ2021 0.49 SEQ2031 0.475 SEQ2062 0.546 SEQ2082 −0.542 SEQ2094 0.648 SEQ2161 0.565 SEQ2176 −0.686 SEQ2177 −0.467 SEQ2192 −0.554 SEQ2204 0.461 SEQ2205 −0.566 SEQ2225 0.569 SEQ2227 0.573 SEQ2230 0.569 SEQ2263 0.532 SEQ2303 0.618 SEQ2309 −0.527 SEQ2326 −0.481 SEQ2346 −0.533 SEQ2390 0.521 SEQ2392 0.567 SEQ2405 −0.499 SEQ2406 0.617 SEQ2444 0.472 SEQ2450 0.451 SEQ2459 −0.656 SEQ2487 −0.497 SEQ2492 0.557 SEQ2497 −0.496 SEQ2513 −0.525 SEQ2542 −0.536 SEQ2576 0.542 SEQ2586 0.524 SEQ2611 0.452 SEQ2636 0.493 SEQ2642 0.514 SEQ2645 0.471 SEQ2647 0.452 SEQ2660 0.483 SEQ2692 0.603 SEQ2740 0.52 SEQ2742 −0.475 SEQ2745 −0.531 SEQ2767 −0.484 SEQ2785 0.457 SEQ2827 −0.493 SEQ2843 0.473 SEQ2857 −0.459 SEQ2860 0.572 SEQ2865 −0.517 SEQ2886 −0.493 SEQ2920 0.453 SEQ2961 0.467 SEQ2974 −0.575 SEQ2978 0.555 SEQ2993 0.453 SEQ3006 −0.476 SEQ3029 0.606 SEQ3046 −0.483 SEQ3058 −0.474 SEQ3079 0.487 SEQ3086 0.468 SEQ3108 0.576 SEQ3124 −0.487 SEQ3128 0.577 SEQ3141 0.527 SEQ3142 0.604 SEQ3156 0.517 SEQ3169 −0.675 SEQ3176 −0.457 SEQ3178 0.46 SEQ3183 −0.582 SEQ3200 0.543 SEQ3207 0.451 SEQ3209 0.533 SEQ3213 0.665

Comparison of the Total RNA-Seq and FiMICS Analysis

Detection level and performance of the lncRNAs can vary in function of the method and number of samples used. FIG. 6 represent the Venn diagram for each analysis using a threshold of LVEF at 40% and 45% for total RNA-Sequencing and FiMICS test. For the comparison of the 4 conditions, 8 lncRNAs are common to all conditions (SEQ1204, SEQ2454, SEQ0334, SEQ1403, SEQ1089, SEQ2692, SEQ2273, and SEQ0502).

An example of probes sequences designed on FiMICS for the first lncRNA (SEQ1204) includes the below sequences;

FIMICS Probe sequence lncRNA GTTCTACTCAAAGGGTCAGTTTAGGGCATAATTAAAGTCAATTACTTT SEQ1204 CTGAAAGGCCATCAGGACAACTGTTAGAGAAAATGATAGCAGCCCCG CACTTGCTGTAGGAATTATTAGCTT CAGGACAACTGTTAGAGAAAATGATAGCAGCCCCGCACTTGCTGTAG SEQ1204 GAATTATTAGCTTGTCAGCCTCCAGGCTTATGGAGACAAAGGATCAAA AAGTTAGAGAGATCCAGGTGTTCAC GTCAGCCTCCAGGCTTATGGAGACAAAGGATCAAAAAGTTAGAGAGA SEQ1204 TCCAGGTGTTCACCTATTTGTTCACTAATTCTTTTATTGTGAGTGTGCA TGTGTGTGGGTGGGTGTGACATTT CTATTTGTTCACTAATTCTTTTATTGTGAGTGTGCATGTGTGTGGGTGG SEQ1204 GTGTGACATTTATTATGAACCAGAGGGCAGGAGCCAGTGACACAGTG GTGCAGAGAATAATCATATTCCCT ATTATGAACCAGAGGGCAGGAGCCAGTGACACAGTGGTGCAGAGAAT SEQ1204 AATCATATTCCCTGCCTTCCTGGGGTCATACAGCTTGGTGGAGGACAC AGATGTGAATTCGGTAATCACTCCA GCCTTCCTGGGGTCATACAGCTTGGTGGAGGACACAGATGTGAATTCG SEQ1204 GTAATCACTCCAATAAATATTCTCCTACAGATGAAGAAAGATGATACG ATGTGATGGACAACAGAGACTTAT ATAAATATTCTCCTACAGATGAAGAAAGATGATACGATGTGATGGAC SEQ1204 AACAGAGACTTATATGGTGGGGTCTGGGCTGGTCTTTCTGAAGCTAAG ACTGGCAGGATGAGCAGGAGTTTGC ATGGTGGGGTCTGGGCTGGTCTTTCTGAAGCTAAGACTGGCAGGATGA SEQ1204 GCAGGAGTTTGCCAGACAAAGAGGAGTGGAGTTGTTTTCCAAACACA TCTCAGCACAAAGTGTTGTCTTTGC CAGACAAAGAGGAGTGGAGTTGTTTTCCAAACACATCTCAGCACAAA SEQ1204 GTGTTGTCTTTGCTGGGAGCTGAAAAAAGATAGTGTGGGCAGAGACC ATTAGGTGAGACGCTTGATATGAGAT TGGGAGCTGAAAAAAGATAGTGTGGGCAGAGACCATTAGGTGAGACG SEQ1204 CTTGATATGAGATACAACCTCAACAGGTGGAAGAAGATCATGAGAGA TGAAGAGAGGAATATAGTACAGCAGA ACAACCTCAACAGGTGGAAGAAGATCATGAGAGATGAAGAGAGGAA SEQ1204 TATAGTACAGCAGAGAGGACACAGAAGCTGACGTCAGGGTGTCTCAG TTTGAAACCAGTGGCCACCCTGTTCCT GAGGACACAGAAGCTGACGTCAGGGTGTCTCAGTTTGAAACCAGTGG SEQ1204 CCACCCTGTTCCTCTCCCATGTGGTCCCATCATGGGCCTCTAGGGTCTG GGATAAGAGGTTAATGAATATCTC CTCCCATGTGGTCCCATCATGGGCCTCTAGGGTCTGGGATAAGAGGTT SEQ1204 AATGAATATCTCATACCCTAAGCAGGGGTGGTCCCTGCACTTTAGCAA AAAGTTAAGGAACTAGGGAAAAGA ATACCCTAAGCAGGGGTGGTCCCTGCACTTTAGCAAAAAGTTAAGGA SEQ1204 ACTAGGGAAAAGAGATGGAAATAATAAAGAGATGGGACAAAGACTTT GAAGACCAAAGCCCCTGGGCTATTCT GATGGAAATAATAAAGAGATGGGACAAAGACTTTGAAGACCAAAGCC SEQ1204 CCTGGGCTATTCTCTTTTTTAAATTTTTTTATTTAAATTTTCATTTATTT TTATCAAGATAGGGTCTCACTAT CTTTTTTAAATTTTTTTATTTAAATTTTCATTTATTTTTATCAAGATAGG SEQ1204 GTCTCACTATGTTGCCCAGGTTGGTCTCAAACTTTTGGCCTAAAGCAA TCCTCCCACCTTGGCCTCCCAA GTTGCCCAGGTTGGTCTCAAACTTTTGGCCTAAAGCAATCCTCCCACC SEQ1204 TTGGCCTCCCAATGTGCTGGGATTACAATGTGAGCCACCACGTCCAGC CTCCTGGGATATTTCTCAATGAAA TGTGCTGGGATTACAATGTGAGCCACCACGTCCAGCCTCCTGGGATAT SEQ1204 TTCTCAATGAAACATTGGATGCCAAGATTGGTTTTGTGCCACATGCCA ATTTCACAGAAGCCAGTCTATGAG CATTGGATGCCAAGATTGGTTTTGTGCCACATGCCAATTTCACAGAAG SEQ1204 CCAGTCTATGAGCCACCAGCTCTACTCAGCAATTACAGTTTCTGGAAC TTTGGCTAAATTCCTGTAGATGCA CCACCAGCTCTACTCAGCAATTACAGTTTCTGGAACTTTGGCTAAATT SEQ1204 CCTGTAGATGCACCACTGCTTGTGGCCTGACTCTTTGCCACCCAAGTG CGCTCAGCCTCCCCTGGGGAGTCT CCACTGCTTGTGGCCTGACTCTTTGCCACCCAAGTGCGCTCAGCCTCCC SEQ1204 CTGGGGAGTCTGCCAGGCTTGCATGGCTCCCACTGCACTTGCTGTGCT GGGACCGAAAACAGTTTTTGTGC GCCAGGCTTGCATGGCTCCCACTGCACTTGCTGTGCTGGGACCGAAAA SEQ1204 CAGTTTTTGTGCCCCTAGCTTAACTCCACTGGATTCATAGAGGCTTTGG CCTCCTCAATGGCTGTCCTGGGA CCCTAGCTTAACTCCACTGGATTCATAGAGGCTTTGGCCTCCTCAATG SEQ1204 GCTGTCCTGGGACAGGGAGGCTGGTTAGCACAATTAACACAACCTGG TCATGCAAGGCATTGATGGTCCGTA CAGGGAGGCTGGTTAGCACAATTAACACAACCTGGTCATGCAAGGCA SEQ1204 TTGATGGTCCGTAACATGAACTTTGACCAGTAGGAGACAGAGAATGG AAAAAAGCCAGCAGATAAATCATCTG ACATGAACTTTGACCAGTAGGAGACAGAGAATGGAAAAAAGCCAGCA SEQ1204 GATAAATCATCTGGCCTTCCTCCCCTATGACAGACTGTTCTGAGCCAC AGTGTTTCACATGTCTTCCTGGAGA GCCTTCCTCCCCTATGACAGACTGTTCTGAGCCACAGTGTTTCACATGT SEQ1204 CTTCCTGGAGATGTCCCACATGACTTGAGCAACCAGCTGGAGCTCTGG AGAAACTGTGGCCATCCTGGTAA TGTCCCACATGACTTGAGCAACCAGCTGGAGCTCTGGAGAAACTGTGG SEQ1204 CCATCCTGGTAACATATGACCTTGTATTTGCTTTCTCTCCTTCCTGCTTT ATTTCCCTATGTCCCTTACTTT CTGTGGCCATCCTGGTAACATATGACCTTGTATTTGCTTTCTCTCCTTC SEQ1204 CTGCTTTATTTCCCTATGTCCCTTACTTTGGTTGTTGGGATTGCACCTCC CAATAAAGCATTAGCATGTCC

Example 5 LncRNA Detection in PAXgene Samples Using a mRNA-seq Protocol

Material and Methods:

Paxgene samples collected at discharge of patient between D3 and D5 from 57 patients with AMI from the MitoCare cohort are used for lncRNA profiling. Mitocare is a multicenter, randomized, double-blind, placebo controlled study. The study population includes AMI patients undergoing PCI, older than 18 years. The primary endpoint is the level of left ventricular ejection fraction (LVEF) less than 40% at 1 month. Demographics data are presented in Table 23.

TABLE 23 Demographic data of patients used from Mitocare study Group 1 Group 2 Group 3 EF <40 41-50 >50 Nb 8 20  29 Age 68.9 60.5 60.0 Male 88% 95% 81% BMI 27.0 28.1 26.6 Systolic Blood 103.0 119.4  116.9 Pressure Diastolic Blood 66.0 71.9 69.6 Pressure Heart Rate 82.3 72.9 66.9

RNA extraction, preparation of sequencing libraires and sequencing are performed as described in Example 3.

Results:

Comparison Between low LVEF (LVEF≤40) and High LVEF (LVEF>40)

In this analysis, the 57 samples AMI were grouped into 2 groups using the threshold of 40% LVEF: low LVEF (LVEF≤40) and high LVEF (LVEF>40). The volcano plot showed the differential expression of lncRNA. 102 lncRNA are differentially expressed and among them, 19 lncRNA have a fold change>2 or <0.5, which are shown in Table 24. 171 lncRNAs with P<0.05 and/or individual AUC>0.7 or <0.3 are listed in Table 25.

TABLE 24 List of 19 lncRNAs which are differentially expressed with a fold change > 2 or <0.5 between the low LVEF group (LVEF ≤ 40) and the high LVEF group (LVEF > 40) lncRNA P-value Fold change Individual AUC SEQ0822 0.0003 0.119 0.717 SEQ1170 0.0012 0.446 0.744 SEQ1755 0.0014 0.434 0.75 SEQ0058 0.0024 0.244 0.709 SEQ2007 0.0027 0.289 0.744 SEQ0430 0.0039 0.394 0.717 SEQ0110 0.0053 0.33 0.745 SEQ1331 0.0071 0.202 0.712 SEQ0388 0.0104 0.294 0.699 SEQ0585 0.0156 2.091 0.194 SEQ0117 0.0174 0.356 0.673 SEQ0415 0.0204 0.407 0.653 SEQ1263 0.0223 0.471 0.672 SEQ0383 0.0269 0.38 0.708 SEQ0187 0.0281 0.436 0.741 SEQ0611 0.0310 0.355 0.656 SEQ2446 0.0364 0.363 0.663 SEQ0548 0.0389 0.488 0.592 SEQ0074 0.0461 12.549 0.221

TABLE 25 List of 171 IncRNA, which are differentially expressed and/or have an AUC >0.7 or <0.3 between the low LVEF group (LVEF ≤ 40) and the high LVEF group (LVEF > 40) IncRNA P-value AUC SEQ0007 0.0583 0.268 SEQ0016 0.0542 0.263 SEQ0058 0.0024 0.709 SEQ0069 0.0124 0.196 SEQ0074 0.0461 0.221 SEQ0110 0.0053 0.745 SEQ0113 0.0656 0.26 SEQ0114 0.0453 0.661 SEQ0117 0.0174 0.673 SEQ0163 0.0042 0.158 SEQ0169 0.0956 0.296 SEQ0187 0.0281 0.741 SEQ0211 0.107 0.276 SEQ0240 0.0145 0.293 SEQ0244 0.0702 0.291 SEQ0246 0.1547 0.758 SEQ0265 0.2273 0.763 SEQ0321 0.0044 0.727 SEQ0329 0.0702 0.26 SEQ0334 0.3913 0.782 SEQ0336 0.1104 0.276 SEQ0348 0.0269 0.314 SEQ0359 0.0171 0.237 SEQ0360 0.0816 0.263 SEQ0367 0.0418 0.666 SEQ0383 0.0269 0.708 SEQ0388 0.0104 0.699 SEQ0409 0.0056 0.73 SEQ0415 0.0204 0.653 SEQ0430 0.0039 0.717 SEQ0435 0.0126 0.214 SEQ0459 0.093 0.733 SEQ0460 0.0418 0.676 SEQ0477 0.0012 0.156 SEQ0493 0.0178 0.722 SEQ0534 0.0453 0.656 SEQ0548 0.0389 0.592 SEQ0559 0.0698 0.273 SEQ0566 0.0805 0.263 SEQ0585 0.0156 0.194 SEQ0598 0.0505 0.263 SEQ0608 0.0648 0.714 SEQ0611 0.031 0.656 SEQ0690 0.0004 0.23 SEQ0720 0.1176 0.73 SEQ0749 0.0645 0.263 SEQ0756 0.0586 0.273 SEQ0784 0.1568 0.283 SEQ0802 0.0345 0.745 SEQ0803 0.0922 0.288 SEQ0807 0.0841 0.281 SEQ0816 0.0431 0.633 SEQ0822 0.0003 0.717 SEQ0845 0.0437 0.671 SEQ0914 0.0473 0.635 SEQ0957 0.0172 0.783 SEQ0968 0.0541 0.27 SEQ0982 0.0477 0.607 SEQ0997 0.0532 0.199 SEQ1023 0.0664 0.263 SEQ1025 0.028 0.204 SEQ1036 0.0415 0.281 SEQ1047 0.0529 0.702 SEQ1065 0.008 0.255 SEQ1066 0.0476 0.27 SEQ1110 0.0596 0.263 SEQ1116 0.0118 0.23 SEQ1151 0.0542 0.255 SEQ1170 0.0012 0.744 SEQ1209 0.0023 0.184 SEQ1211 0.0298 0.758 SEQ1252 0.0275 0.222 SEQ1263 0.0223 0.672 SEQ1265 0.1112 0.291 SEQ1285 0.0491 0.626 SEQ1290 0.0851 0.288 SEQ1300 0.0452 0.625 SEQ1319 0.0549 0.273 SEQ1325 0.0718 0.288 SEQ1331 0.0071 0.712 SEQ1386 0.0312 0.676 SEQ1406 0.0161 0.689 SEQ1421 0.1131 0.264 SEQ1451 0.0196 0.709 SEQ1458 0.0329 0.635 SEQ1460 0.1292 0.298 SEQ1483 0.0008 0.176 SEQ1507 0.0098 0.293 SEQ1510 0.0003 0.765 SEQ1511 0.0166 0.212 SEQ1519 0.0066 0.681 SEQ1531 0.0143 0.694 SEQ1533 0.0079 0.699 SEQ1536 0.011 0.196 SEQ1591 0.0256 0.661 SEQ1632 0.0308 0.283 SEQ1638 0.0316 0.24 SEQ1669 0.0466 0.247 SEQ1705 0.1096 0.288 SEQ1755 0.0014 0.75 SEQ1777 0.0585 0.255 SEQ1795 0.0046 0.199 SEQ1809 0.041 0.265 SEQ1822 0.0575 0.268 SEQ1826 0.101 0.298 SEQ1885 0.0416 0.577 SEQ1936 0.0348 0.263 SEQ1949 0.0036 0.676 SEQ1973 0.0075 0.148 SEQ1976 0.0367 0.643 SEQ2003 0.0712 0.714 SEQ2007 0.0027 0.744 SEQ2025 0.028 0.676 SEQ2042 0.0214 0.704 SEQ2057 0.025 0.245 SEQ2070 0.0208 0.714 SEQ2084 0.0164 0.23 SEQ2095 0.082 0.288 SEQ2150 0.0561 0.224 SEQ2229 0.5132 0.707 SEQ2254 0.0465 0.714 SEQ2277 0.0804 0.276 SEQ2291 0.0315 0.27 SEQ2325 0.0406 0.651 SEQ2369 0.0483 0.296 SEQ2371 0.3109 0.745 SEQ2387 0.1645 0.296 SEQ2436 0.0619 0.247 SEQ2446 0.0364 0.663 SEQ2487 0.036 0.712 SEQ2490 0.0171 0.268 SEQ2506 0.4184 0.704 SEQ2522 0.0929 0.281 SEQ2540 0.0604 0.27 SEQ2563 0.0566 0.217 SEQ2571 0.0761 0.189 SEQ2579 0.0415 0.263 SEQ2588 0.0888 0.296 SEQ2647 0.0615 0.283 SEQ2651 0.1479 0.286 SEQ2672 0.0525 0.255 SEQ2675 0.0735 0.286 SEQ2692 0.0639 0.298 SEQ2697 0.0147 0.237 SEQ2701 0.0295 0.245 SEQ2720 0.0434 0.255 SEQ2727 0.0337 0.24 SEQ2755 0.1095 0.709 SEQ2779 0.0642 0.291 SEQ2783 0.0001 0.839 SEQ2794 0.0636 0.298 SEQ2803 0.1414 0.293 SEQ2814 0.1279 0.298 SEQ2855 0.022 0.217 SEQ2863 0.0823 0.298 SEQ2878 0.0148 0.191 SEQ2887 0.082 0.298 SEQ2928 0.0927 0.286 SEQ2967 0.0218 0.296 SEQ2992 0.0096 0.209 SEQ3011 0.0128 0.189 SEQ3029 0.0721 0.268 SEQ3080 0.0223 0.24 SEQ3118 0.0086 0.194 SEQ3128 0.0276 0.224 SEQ3154 0.0255 0.288 SEQ3160 0.02 0.247 SEQ3184 0.1028 0.26 SEQ3186 0.0802 0.291 SEQ3203 0.0226 0.235 SEQ3235 0.0114 0.232

For this classification, the variable selection was performed by using a Random Forest model. A combination of 20 pre-selected lncRNA through a Random Forest Classifier (Table 26) is the best predictive model obtained here. The lncRNAs were selected using a random forest algorithm. The model was produced with Naives Bayes algorithm. This model has an area under the receiver-operating characteristic curve (AUC) of 0.834, an accuracy of 0.895, a sensitivity of 0.918, a specificity of 0.75, a Positive Predictive Value (PPV) of 0.957 and Negative Predictive Value (PNV) of 0.6. The confusion matrix is presented in Table 27.

TABLE 26 List of 20 pre-selected lncRNA through a Random Forest Classifier for the classification low LVEF (LVEF ≤ 40) and high LVEF (LVEF > 40) lncRNA Rank in the model SEQ0190 1 SEQ0359 2 SEQ0776 3 SEQ1421 4 SEQ1795 5 SEQ0477 6 SEQ1511 7 SEQ0435 8 SEQ1418 9 SEQ1025 10 SEQ0265 11 SEQ1311 12 SEQ2540 13 SEQ2323 14 SEQ3011 15 SEQ2447 16 SEQ2863 17 SEQ2697 18 SEQ3128 19 SEQ2265 20

TABLE 27 Confusion matrix of the best model for this classification Low LVEF predicted High LVEF predicted Low LVEF True 6 2 High LVEF True 4 45

Comparison Between Low LVEF (LVEF≤45) and High LVEF (LVEF>45)

In this analysis, the 57 samples AMI were grouped into 2 groups using the threshold of 45% LVEF: low LVEF (LVEF≤45) and high LVEF (LVEF>45). The volcano plot showed the differential expression of lncRNA. 110 lncRNA are differentially expressed and among them 11 lncRNA have a fold change>2 or <0.5, which are in Table 28. 112 lncRNAs with P<0.05 and/or individual AUC>0.7 or <0.3 are listed in Table 29.

TABLE 28 List of 11 lncRNAs which are differentially expressed with a fold change > 2 or <0.5between the low LVEF group (LVEF ≤ 40) and the high LVEF group (LVEF > 40) lncRNA P-Value foldchange AUC SEQ1755 0.00017 0.460 0.740 SEQ1331 0.00072 0.243 0.710 SEQ1372 0.00560 0.437 0.695 SEQ1341 0.01608 0.364 0.664 SEQ0173 0.02953 0.481 0.654 SEQ0611 0.03193 0.434 0.645 SEQ1602 0.03198 2.164 0.301 SEQ0442 0.04288 0.477 0.635 SEQ0117 0.04364 0.494 0.607 SEQ0074 0.04683 7.908 0.346 SEQ2168 0.04815 0.452 0.627

TABLE 29 List of 112 IncRNAs which are differentially expressed and/or have an AUC >0.7 or <0.3 between the low LVEF group (LVEF ≤ 40) and the high LVEF group (LVEF > 40) IncRNA P-Value AUC SEQ0007 0.028 0.33 SEQ0036 0.057 0.72 SEQ0064 0.031 0.65 SEQ0074 0.047 0.35 SEQ0079 0.004 0.73 SEQ0117 0.044 0.61 SEQ0137 0.012 0.72 SEQ0163 0.017 0.30 SEQ0169 0.024 0.29 SEQ0173 0.030 0.65 SEQ0240 0.017 0.31 SEQ0265 0.024 0.73 SEQ0269 0.016 0.31 SEQ0359 0.003 0.29 SEQ0376 0.013 0.29 SEQ0440 0.009 0.65 SEQ0442 0.043 0.64 SEQ0446 0.049 0.32 SEQ0476 0.016 0.66 SEQ0477 0.048 0.31 SEQ0493 0.020 0.65 SEQ0534 0.040 0.65 SEQ0535 0.010 0.70 SEQ0545 0.009 0.27 SEQ0559 0.017 0.30 SEQ0564 0.040 0.63 SEQ0609 0.046 0.66 SEQ0611 0.032 0.65 SEQ0627 0.015 0.70 SEQ0690 0.019 0.30 SEQ0709 0.031 0.64 SEQ0720 0.008 0.71 SEQ0749 0.031 0.29 SEQ0756 0.023 0.33 SEQ0762 0.021 0.31 SEQ0802 0.019 0.68 SEQ0845 0.013 0.68 SEQ0914 0.039 0.62 SEQ1025 0.026 0.31 SEQ1042 0.012 0.26 SEQ1047 0.044 0.66 SEQ1065 0.011 0.29 SEQ1117 0.032 0.70 SEQ1123 0.028 0.32 SEQ1150 0.030 0.66 SEQ1158 0.032 0.65 SEQ1211 0.027 0.64 SEQ1228 0.011 0.65 SEQ1290 0.049 0.30 SEQ1300 0.024 0.62 SEQ1331 0.001 0.71 SEQ1341 0.016 0.66 SEQ1372 0.006 0.70 SEQ1403 0.010 0.66 SEQ1406 0.016 0.68 SEQ1446 0.032 0.30 SEQ1458 0.033 0.67 SEQ1475 0.012 0.70 SEQ1483 0.025 0.30 SEQ1511 0.007 0.30 SEQ1518 0.023 0.31 SEQ1519 0.017 0.68 SEQ1533 0.004 0.73 SEQ1536 0.026 0.32 SEQ1539 0.002 0.73 SEQ1591 0.043 0.61 SEQ1596 0.044 0.63 SEQ1602 0.032 0.30 SEQ1739 0.002 0.70 SEQ1755 0.000 0.74 SEQ1762 0.024 0.69 SEQ1766 0.037 0.32 SEQ1795 0.026 0.34 SEQ1930 0.010 0.30 SEQ1973 0.016 0.29 SEQ2003 0.025 0.68 SEQ2084 0.024 0.30 SEQ2113 0.021 0.32 SEQ2149 0.031 0.33 SEQ2168 0.048 0.63 SEQ2186 0.042 0.63 SEQ2218 0.021 0.66 SEQ2254 0.033 0.67 SEQ2323 0.050 0.65 SEQ2347 0.019 0.69 SEQ2369 0.047 0.34 SEQ2426 0.030 0.62 SEQ2436 0.020 0.29 SEQ2471 0.007 0.73 SEQ2502 0.033 0.33 SEQ2540 0.008 0.26 SEQ2647 0.027 0.31 SEQ2684 0.028 0.27 SEQ2697 0.004 0.28 SEQ2727 0.008 0.30 SEQ2783 0.018 0.68 SEQ2850 0.045 0.33 SEQ2863 0.040 0.32 SEQ3011 0.007 0.25 SEQ3049 0.047 0.59 SEQ3051 0.015 0.30 SEQ3069 0.040 0.61 SEQ3106 0.035 0.31 SEQ3118 0.028 0.33 SEQ3128 0.007 0.28 SEQ3137 0.042 0.62 SEQ3160 0.015 0.31 SEQ3184 0.184 0.30 SEQ3186 0.035 0.30 SEQ3193 0.026 0.32 SEQ3203 0.031 0.32 SEQ3235 0.027 0.31

For this classification, the variable selection was performed by using a Random Forest model. A combination of 11 pre-selected lncRNA through a Random Forest Classifier (Table 30) is the best predictive model obtained here. The lncRNAs were selected using a random forest algorithm. This model has an area under the receiver-operating characteristic curve (AUC) of 0.905, an accuracy of 0.807, a sensitivity of 0.927, a specificity of 0.5, a Positive Predictive Value (PPV) of 0.826 and Negative Predictive Value (PNV) of 0.727. The confusion matrix is presented in Table 31.

TABLE 30 List of 11 pre-selected lncRNA through a Random Forest Classifier for the classification low LVEF (LVEF ≤ 45) and high LVEF (LVEF > 45) lncRNA Rank in the model SEQ2540 1 SEQ0545 2 SEQ1766 3 SEQ3011 4 SEQ0968 5 SEQ2371 6 SEQ1533 7 SEQ0749 8 SEQ0609 9 SEQ1446 10 SEQ2986 11

TABLE 31 Confusion matrix of the best model for this classification Low LVEF predicted High LVEF predicted Low LVEF True 8 8 High LVEF True 3 38

Example 6 Analysis Control Subject Versus AMI Patients at D0 Total Seq on Cardiac Enriched lncRNAs

Quantification of lncRNAs in body fluids including but not limited to whole blood, serum, plasma, urine, saliva is a non-invasive way to develop a diagnostic test to use in clinics. The expression of circulating lncRNA is studied in serum samples from patients with AMI and control subjects.

Serum samples collected at D0 of patient with AMI from the MitoCare cohort and control subject of chronobiological study are used for lncRNA profiling. Mitocare demographics are presented in Table 3. Technical workflow is identical as described in Example 3.

Results:

Comparison Between Control Subject Versus AMI Patients at D0

First, samples are grouped into 2 group by a dichotomized variable: patients with cardiac disorder (AMI) and subjects with no cardiac disease. We found that 1736 lncRNAs are differentially expressed (p<0.05). Most of the lncRNAs are overexpressed in patient undergoing an AMI. We show here that the lncRNAs identified in heart biopsie are biomarkers for diagnosis of heart diseases. By selecting lncRNAs with p<0.01; a fold change>2 or <0.5 and an individual AUC>0.8 or <0.2, we identified a list of 288 lncRNAs that can diagnose AMI or heart diseases (Table 32).

TABLE 32 list of 288 IncRNAs differentially expressed, with a fold change >2 or <0.5 and an individual AUC >0.8 or <0.2. IncRNA P-Value Fold change auc SEQ0014 0.00009 0.49 0.19 SEQ0020 0.00002 0.35 0.13 SEQ0027 0.00005 0.31 0.16 SEQ0042 0.00000 0.50 0.11 SEQ0051 0.00315 10.58 0.85 SEQ0055 0.00001 0.42 0.13 SEQ0085 0.00001 0.29 0.13 SEQ0097 0.00012 0.49 0.17 SEQ0107 0.00009 0.26 0.16 SEQ0130 0.00012 0.24 0.16 SEQ0138 0.00007 0.47 0.17 SEQ0151 0.00000 0.26 0.09 SEQ0155 0.00007 0.32 0.15 SEQ0176 0.00025 0.44 0.17 SEQ0190 0.00000 0.34 0.05 SEQ0199 0.00030 0.46 0.19 SEQ0206 0.00003 0.40 0.16 SEQ0210 0.00001 0.48 0.12 SEQ0215 0.00003 0.27 0.16 SEQ0226 0.00000 0.46 0.02 SEQ0227 0.00001 0.46 0.15 SEQ0236 0.00009 0.44 0.17 SEQ0251 0.00010 0.26 0.20 SEQ0263 0.00032 0.42 0.20 SEQ0268 0.00001 0.43 0.14 SEQ0281 0.00003 0.44 0.14 SEQ0293 0.00000 0.12 0.16 SEQ0325 0.00100 0.20 0.18 SEQ0330 0.00008 0.27 0.16 SEQ0350 0.00000 0.38 0.10 SEQ0365 0.00001 0.47 0.14 SEQ0368 0.00022 0.32 0.20 SEQ0372 0.00009 0.35 0.18 SEQ0374 0.00032 0.23 0.17 SEQ0383 0.00054 0.49 0.19 SEQ0387 0.00006 0.41 0.18 SEQ0396 0.00019 0.34 0.17 SEQ0402 0.00021 0.36 0.20 SEQ0439 0.00029 0.45 0.19 SEQ0465 0.00000 0.31 0.05 SEQ0486 0.00041 0.46 0.19 SEQ0494 0.00003 0.42 0.16 SEQ0499 0.00000 0.38 0.13 SEQ0507 0.00001 0.17 0.13 SEQ0511 0.00016 0.44 0.17 SEQ0523 0.00000 0.21 0.01 SEQ0538 0.00059 0.29 0.20 SEQ0559 0.00016 0.47 0.19 SEQ0560 0.00027 0.34 0.19 SEQ0564 0.00000 0.28 0.08 SEQ0572 0.00000 0.21 0.09 SEQ0589 0.00018 0.48 0.19 SEQ0594 0.00000 20.93 1.00 SEQ0597 0.00009 0.17 0.09 SEQ0599 0.00001 0.40 0.12 SEQ0639 0.00005 2.02 0.85 SEQ0647 0.00000 0.43 0.10 SEQ0657 0.00000 0.49 0.08 SEQ0662 0.00024 0.31 0.17 SEQ0664 0.00001 0.42 0.15 SEQ0668 0.00015 0.29 0.18 SEQ0674 0.00000 0.47 0.13 SEQ0685 0.00009 0.46 0.17 SEQ0696 0.00010 0.29 0.16 SEQ0697 0.00000 0.23 0.12 SEQ0707 0.00000 0.43 0.05 SEQ0710 0.00003 0.40 0.17 SEQ0714 0.00002 0.37 0.11 SEQ0745 0.00044 0.38 0.19 SEQ0755 0.00000 0.19 0.08 SEQ0772 0.00006 2.32 0.82 SEQ0804 0.00012 0.35 0.20 SEQ0809 0.00075 0.20 0.19 SEQ0818 0.00000 0.46 0.01 SEQ0839 0.00000 0.42 0.04 SEQ0846 0.00000 0.41 0.03 SEQ0862 0.00024 0.32 0.19 SEQ0866 0.00000 0.25 0.11 SEQ0884 0.00004 0.44 0.17 SEQ0886 0.00001 0.32 0.12 SEQ0899 0.00000 0.38 0.10 SEQ0916 0.00000 0.41 0.03 SEQ0917 0.00003 0.33 0.15 SEQ0936 0.00005 0.45 0.17 SEQ0939 0.00009 0.29 0.19 SEQ0949 0.00000 0.45 0.05 SEQ0955 0.00023 0.37 0.16 SEQ0970 0.00001 0.46 0.14 SEQ0983 0.00000 0.46 0.11 SEQ0984 0.00000 0.12 0.09 SEQ0986 0.00017 0.50 0.20 SEQ0989 0.00027 0.32 0.19 SEQ0990 0.00000 0.11 0.11 SEQ0995 0.00007 0.31 0.17 SEQ1001 0.00004 0.44 0.17 SEQ1008 0.00000 0.47 0.11 SEQ1028 0.00010 0.31 0.19 SEQ1047 0.00005 0.43 0.19 SEQ1051 0.00002 0.49 0.16 SEQ1055 0.00000 0.46 0.03 SEQ1066 0.00000 0.48 0.09 SEQ1072 0.00000 0.29 0.07 SEQ1086 0.00000 0.31 0.08 SEQ1088 0.00001 0.20 0.15 SEQ1106 0.00004 0.40 0.14 SEQ1113 0.00000 0.34 0.13 SEQ1115 0.00022 0.43 0.19 SEQ1116 0.00000 0.49 0.03 SEQ1131 0.00000 0.25 0.05 SEQ1135 0.00024 0.40 0.19 SEQ1138 0.00000 0.25 0.10 SEQ1142 0.00037 7.14 0.97 SEQ1146 0.00008 0.38 0.17 SEQ1180 0.00005 0.18 0.17 SEQ1184 0.00000 0.36 0.07 SEQ1211 0.00000 0.47 0.02 SEQ1220 0.00000 0.41 0.12 SEQ1239 0.00001 0.43 0.14 SEQ1253 0.00030 0.28 0.17 SEQ1276 0.00164 0.40 0.19 SEQ1291 0.00000 0.38 0.08 SEQ1297 0.00000 0.43 0.02 SEQ1301 0.00011 0.25 0.16 SEQ1306 0.00015 0.15 0.17 SEQ1307 0.00005 0.30 0.16 SEQ1314 0.00001 0.46 0.14 SEQ1320 0.00004 0.18 0.12 SEQ1336 0.00006 0.48 0.17 SEQ1350 0.00008 0.48 0.19 SEQ1357 0.00008 0.29 0.13 SEQ1367 0.00010 0.34 0.16 SEQ1372 0.00063 0.46 0.19 SEQ1374 0.00000 0.48 0.02 SEQ1393 0.00000 0.37 0.12 SEQ1404 0.00001 0.42 0.14 SEQ1415 0.00000 0.23 0.06 SEQ1424 0.00024 0.31 0.17 SEQ1434 0.00005 0.26 0.17 SEQ1469 0.00000 0.45 0.03 SEQ1477 0.00000 2.06 0.90 SEQ1484 0.00000 0.42 0.04 SEQ1492 0.00007 0.26 0.18 SEQ1499 0.00000 0.37 0.09 SEQ1502 0.00004 0.22 0.17 SEQ1509 0.00000 0.32 0.12 SEQ1523 0.00027 0.31 0.16 SEQ1532 0.00005 0.17 0.16 SEQ1534 0.00000 0.48 0.00 SEQ1537 0.00009 0.40 0.15 SEQ1567 0.00012 0.47 0.16 SEQ1572 0.00003 0.43 0.15 SEQ1582 0.00026 0.13 0.17 SEQ1585 0.00026 2.17 0.83 SEQ1587 0.00000 0.40 0.10 SEQ1597 0.00009 0.19 0.16 SEQ1601 0.00001 6.65 0.88 SEQ1608 0.00046 0.44 0.20 SEQ1612 0.00000 0.08 0.10 SEQ1624 0.00000 0.41 0.05 SEQ1625 0.00000 0.21 0.05 SEQ1638 0.00001 2.06 0.85 SEQ1646 0.00000 0.42 0.08 SEQ1647 0.00000 0.44 0.05 SEQ1652 0.00539 0.21 0.15 SEQ1670 0.00036 0.34 0.20 SEQ1680 0.00003 0.26 0.13 SEQ1716 0.00000 0.12 0.10 SEQ1717 0.00062 0.05 0.15 SEQ1719 0.00038 0.30 0.20 SEQ1721 0.00001 0.37 0.15 SEQ1731 0.00000 0.06 0.09 SEQ1732 0.00002 0.45 0.14 SEQ1735 0.00000 0.19 0.04 SEQ1739 0.00001 0.33 0.10 SEQ1747 0.00001 0.37 0.15 SEQ1753 0.00001 0.43 0.12 SEQ1761 0.00057 0.48 0.19 SEQ1764 0.00112 0.32 0.19 SEQ1774 0.00028 0.32 0.19 SEQ1777 0.00000 0.43 0.12 SEQ1810 0.00010 0.50 0.17 SEQ1837 0.00009 0.34 0.14 SEQ1859 0.00000 0.43 0.13 SEQ1874 0.00030 0.43 0.20 SEQ1888 0.00000 0.34 0.09 SEQ1891 0.00006 0.44 0.18 SEQ1893 0.00005 0.06 0.13 SEQ1900 0.00041 0.40 0.20 SEQ1927 0.00000 0.48 0.09 SEQ1947 0.00000 0.33 0.12 SEQ1963 0.00000 0.40 0.09 SEQ1975 0.00024 0.26 0.18 SEQ1985 0.00468 0.46 0.20 SEQ1991 0.00000 0.33 0.10 SEQ1992 0.00000 0.47 0.11 SEQ1994 0.00000 0.43 0.06 SEQ1998 0.00000 0.48 0.05 SEQ1999 0.00002 0.41 0.13 SEQ2020 0.00001 0.39 0.13 SEQ2043 0.00001 0.11 0.10 SEQ2059 0.00005 0.38 0.16 SEQ2065 0.00000 0.43 0.02 SEQ2070 0.00000 0.32 0.12 SEQ2071 0.00001 0.37 0.13 SEQ2077 0.00005 0.10 0.07 SEQ2082 0.00000 0.42 0.12 SEQ2085 0.00002 0.28 0.14 SEQ2093 0.00000 0.26 0.10 SEQ2108 0.00000 0.21 0.07 SEQ2127 0.00322 0.36 0.16 SEQ2129 0.00000 0.47 0.13 SEQ2133 0.00061 0.45 0.19 SEQ2148 0.00000 2.04 0.89 SEQ2156 0.00010 0.18 0.16 SEQ2161 0.00000 2.05 0.93 SEQ2163 0.00000 0.19 0.05 SEQ2173 0.00000 0.46 0.04 SEQ2184 0.00006 0.32 0.14 SEQ2192 0.00000 0.47 0.11 SEQ2196 0.00005 0.44 0.16 SEQ2198 0.00010 0.49 0.18 SEQ2207 0.00004 0.24 0.13 SEQ2245 0.00002 0.38 0.16 SEQ2250 0.00000 0.49 0.05 SEQ2260 0.00024 2.31 0.82 SEQ2280 0.00012 0.12 0.12 SEQ2295 0.00000 0.41 0.13 SEQ2310 0.00002 0.21 0.16 SEQ2343 0.00017 0.33 0.20 SEQ2373 0.00000 0.47 0.03 SEQ2406 0.00014 2.65 0.81 SEQ2420 0.00001 0.40 0.12 SEQ2462 0.00000 0.36 0.08 SEQ2479 0.00063 0.49 0.19 SEQ2488 0.00000 0.40 0.09 SEQ2489 0.00018 2.10 0.81 SEQ2571 0.00001 0.36 0.14 SEQ2584 0.00000 0.45 0.07 SEQ2603 0.00000 0.42 0.02 SEQ2676 0.00000 0.49 0.12 SEQ2682 0.00000 0.46 0.05 SEQ2766 0.00001 0.19 0.12 SEQ2832 0.00064 0.45 0.19 SEQ2842 0.00011 0.40 0.19 SEQ2868 0.00001 0.16 0.07 SEQ2904 0.00242 0.20 0.14 SEQ2924 0.00000 2.10 0.87 SEQ2939 0.00000 0.49 0.13 SEQ2946 0.00000 0.41 0.04 SEQ2985 0.00000 0.47 0.03 SEQ2996 0.00047 0.15 0.17 SEQ3006 0.00002 0.43 0.16 SEQ3073 0.00037 0.37 0.19 SEQ3133 0.00000 0.39 0.02 SEQ3139 0.00000 0.28 0.07 SEQ3198 0.00000 0.46 0.08 SEQ3212 0.00000 0.49 0.09 SEQ3220 0.00033 0.41 0.19

Correlation Between lncRNA Expression at D0 and LVEF at 3 Days

In order to predict outcome of patient suffering from AMI at day 3 and recovery of the patients, LVEF at day 3 is considered as continuous value and spearman correlation is performed between lncRNA expression at D0 and LVEF at day 3. We found that 72 lncRNAs present a correlation factor over 0.45 or below −0.45 as represented in Table 33. These lncRNAs can be used as predictor of outcome 3 days after AMI to evaluate LVEF.

TABLE 33 72 lncRNAs with spearman correlation factor over 0.45 or below −0.45 wit LVEF at D 3. lncRNA Correlation SEQ0026 −0.475 SEQ0090 −0.530 SEQ0097 0.453 SEQ0103 −0.639 SEQ0131 −0.512 SEQ0212 −0.454 SEQ0242 0.517 SEQ0255 −0.559 SEQ0266 −0.649 SEQ0433 −0.504 SEQ0489 −0.454 SEQ0563 0.494 SEQ0573 −0.537 SEQ0595 −0.605 SEQ0602 0.557 SEQ0718 0.593 SEQ0721 −0.472 SEQ0741 −0.598 SEQ0777 −0.617 SEQ0786 −0.529 SEQ0900 −0.469 SEQ0903 −0.629 SEQ0947 −0.473 SEQ1021 −0.508 SEQ1034 0.453 SEQ1045 −0.474 SEQ1051 −0.499 SEQ1076 −0.652 SEQ1176 −0.512 SEQ1245 −0.568 SEQ1295 0.599 SEQ1373 0.533 SEQ1391 0.500 SEQ1392 −0.474 SEQ1482 −0.492 SEQ1514 −0.453 SEQ1571 −0.476 SEQ1579 0.506 SEQ1637 −0.469 SEQ1830 −0.477 SEQ1847 −0.465 SEQ1848 0.666 SEQ1932 −0.531 SEQ1947 −0.477 SEQ2091 −0.553 SEQ2095 −0.496 SEQ2244 −0.458 SEQ2258 −0.595 SEQ2273 0.502 SEQ2307 −0.547 SEQ2312 0.574 SEQ2329 0.545 SEQ2371 0.493 SEQ2387 0.594 SEQ2390 0.644 SEQ2396 −0.513 SEQ2429 0.529 SEQ2452 0.452 SEQ2517 0.531 SEQ2523 −0.479 SEQ2549 −0.520 SEQ2628 −0.505 SEQ2674 −0.492 SEQ2709 −0.487 SEQ2827 0.501 SEQ2829 0.587 SEQ2858 −0.457 SEQ2900 0.470 SEQ2907 −0.481 SEQ2996 −0.514 SEQ3054 0.455 SEQ3166 0.551

Among these lncRNA, 4 lncRNA (SEQ0097, SEQ1947, SEQ1051 and SEQ2996) are differentially expressed between controls and AMI, and are correlated to LVEF value at D3.

Example 7 Analysis of Gencode lncRNAs from Serum RNA-Seq Data

Quantification of lncRNAs in body fluids including but not limited to whole blood, serum, plasma, urine, saliva is a non-invasive way to develop a diagnostic test to use in clinics. The expression of circulating lncRNA is studied in serum samples from patients with AMI and control subjects.

Serum samples collected at D0 and D3-D5 of patient with AMI from the MitoCare cohort and control subject of chronobiological study are used for lncRNA profiling. Mitocare demographics are presented in Table 3. Technical workflow is identical as described in Example 3 and sequencing data are aligned against Gencode database from LNCipedia 5.0. Cardiac enriched lncRNAs (SEQ0001 to SEQ3238) are removed from the analysis. A threshold of 10 CPM in half of samples in one group is applied to consider the lncRNA as positive. In this analysis, focus is done on circulating lncRNAs to be used as biomarkers for the prediction and monitoring of Left Ventricular Remodeling and development of heart failure.

Comparison Between Low LVEF (LVEF≤40%) and High LVEF (LVEF>40%) at D3-D5 Serum Samples

First, samples are classified into 2 group by a dichotomized variable: 1-month LVEF<40% considered as LV dysfunction (Ventricular remodeling) and 1-month LVEF>40% considered as preserved LV function.

291 lncRNA are differentially expressed and among these, 82 lncRNA are differentially expressed and have a fold change>2 or <0.5 between the low LVEF (LVEF≤40%) and the high LVEF (LVEF>40%). The p-value and the fold-change of these lncRNA are listed in the Table 34. 468 lncRNAs which have a p<0.05 and/or an individual AUC>0.7 or <0.3 are listed in Table 35.

TABLE 34 List of 86 lncRNAs from Gencode database which are differentially expressed (p < 0.05) and have a fold change > 2 or <0.5 between the low LVEF group (LVEF ≤ 40%) and the high LVEF group (LVEF > 40%) lncRNA P value foldchange ENST00000491676.1 0.002 0.461 ENST00000512458.1 0.002 0.211 ENST00000485020.1 0.002 3.802 ENST00000487814.1 0.002 2.091 ENST00000515306.1 0.003 3.302 ENST00000426551.1 0.004 0.244 ENST00000412944.1 0.004 8.646 ENST00000553319.1 0.004 0.493 ENST00000421563.1 0.005 0.435 ENST00000427732.1 0.006 5.310 ENST00000506068.1 0.006 5.486 ENST00000417420.1 0.006 5.855 ENST00000514942.2 0.007 2.865 ENST00000461943.1 0.009 2.816 ENST00000507932.1 0.009 0.238 ENST00000456255.1 0.010 0.295 ENST00000519929.1 0.011 0.357 ENST00000466034.1 0.013 6.486 ENST00000399152.2 0.013 3.882 ENST00000422417.1 0.014 0.262 ENST00000503037.1 0.015 0.430 ENST00000515811.1 0.015 3.365 ENST00000502861.1 0.016 2.281 ENST00000455541.1 0.016 0.382 ENST00000424592.1 0.016 2.843 ENST00000431911.1 0.017 0.422 ENST00000452618.1 0.017 2.526 ENST00000437488.1 0.018 0.333 ENST00000443066.2 0.018 3.846 ENST00000457169.1 0.018 10.873 ENST00000447761.1 0.019 2.455 ENST00000527035.1 0.019 0.313 ENST00000522525.1 0.021 2.384 ENST00000602445.1 0.022 13.038 ENST00000431569.1 0.022 4.473 ENST00000609450.1 0.022 0.498 ENST00000501965.2 0.022 2.161 ENST00000441026.1 0.022 2.312 ENST00000432125.2 0.022 2.253 ENST00000609549.1 0.023 0.393 ENST00000514526.1 0.023 0.286 ENST00000510946.1 0.024 3.217 ENST00000521819.1 0.025 0.140 ENST00000608774.1 0.025 0.481 ENST00000601586.1 0.026 0.399 ENST00000508847.1 0.026 0.229 ENST00000421696.2 0.026 2.796 ENST00000601913.1 0.028 3.766 ENST00000494900.1 0.029 2.198 ENST00000434207.1 0.030 2.133 ENST00000452809.1 0.031 2.428 ENST00000498413.1 0.032 0.321 ENST00000507957.1 0.034 2.706 ENST00000443562.1 0.034 0.355 ENST00000577528.1 0.034 0.218 ENST00000439964.1 0.035 0.367 ENST00000515184.1 0.035 0.469 ENST00000452795.2 0.035 0.392 ENST00000427213.1 0.036 2.863 ENST00000416506.1 0.037 0.411 ENST00000432038.1 0.037 0.488 ENST00000521805.1 0.037 0.403 ENST00000498480.1 0.038 0.492 ENST00000455988.1 0.038 3.218 ENST00000606056.1 0.038 0.331 ENST00000509057.1 0.038 0.457 ENST00000465215.1 0.039 0.122 ENST00000514368.1 0.040 0.349 ENST00000585826.1 0.040 3.226 ENST00000472821.1 0.041 3.001 ENST00000588108.1 0.041 0.386 ENST00000421640.1 0.041 2.670 ENST00000437290.2 0.042 0.193 ENST00000415629.2 0.043 0.118 ENST00000489690.1 0.043 0.481 ENST00000513219.1 0.043 0.416 ENST00000419614.1 0.043 2.574 ENST00000604677.1 0.044 3.502 ENST00000440574.1 0.048 2.392 ENST00000435643.1 0.048 0.212 ENST00000587568.1 0.050 3.194 ENST00000413525.1 0.050 4.403

TABLE 35 List of 468 IncRNA from Gencode database which are differentially expressed (p < 0.05) and/or have an AUC >0.7 or <0.3 between the low LVEF group (LVEF ≤ 40%) and the high LVEF group (LVEF > 40%) IncRNA p Value auc ENST00000425754.1 00000 00850 ENST00000609071.1 00000 00875 ENST00000503929.1 00000 00825 ENST00000562952.1 00001 00830 ENST00000587099.1 00001 00860 ENST00000424895.1 00001 00825 ENST00000608537.1 00001 00810 ENST00000414309.1 00002 00850 ENST00000491676.1 00002 00160 ENST00000412134.1 00002 00805 ENST00000565538.1 00002 00810 ENST00000508752.1 00002 00795 ENST00000512458.1 00002 00123 ENST00000485020.1 00002 00810 ENST00000487814.1 00002 00820 ENST00000598757.1 00002 00170 ENST00000515306.1 00003 00790 ENST00000443613.2 00003 00190 ENST00000507344.1 00004 00815 ENST00000426551.1 00004 00170 ENST00000412944.1 00004 00720 ENST00000513958.1 00004 00195 ENST00000511064.1 00004 00790 ENST00000448901.1 00004 00795 ENST00000553319.1 00004 00150 ENST00000421563.1 00005 00205 ENST00000497573.1 00005 00140 ENST00000456026.1 00005 00775 ENST00000427732.1 00006 00745 ENST00000506068.1 00006 00730 ENST00000512712.2 00006 00200 ENST00000417420.1 00006 00735 ENST00000568686.1 00006 00245 ENST00000543490.1 00006 00785 ENST00000503815.1 00007 00185 ENST00000565044.1 00007 00195 ENST00000514942.2 00007 00735 ENST00000607216.1 00007 00160 ENST00000412294.1 00007 00785 ENST00000430666.1 00007 00205 ENST00000415330.2 00007 00200 ENST00000429666.1 00008 00215 ENST00000499713.2 00008 00220 ENST00000608574.1 00008 00170 ENST00000420365.1 00008 00220 ENST00000421998.1 00008 00240 ENST00000424244.1 00009 00265 ENST00000552220.1 00009 00795 ENST00000428156.1 00009 00770 ENST00000429725.1 00009 00780 ENST00000461943.1 00009 00715 ENST00000508572.1 00009 00225 ENST00000507932.1 00009 00205 ENST00000418602.1 00010 00250 ENST00000505680.1 00010 00755 ENST00000419578.1 00010 00785 ENST00000475939.1 00010 00195 ENST00000456255.1 00010 00193 ENST00000610058.1 00011 00775 ENST00000607786.1 00011 00735 ENST00000439898.1 00011 00255 ENST00000519929.1 00011 00185 ENST00000447181.1 00011 00275 ENST00000504287.1 00012 00745 ENST00000435552.1 00012 00260 ENST00000366441.2 00012 00745 ENST00000441790.1 00012 00780 ENST00000505018.1 00012 00755 ENST00000496733.2 00012 00730 ENST00000440322.1 00012 00770 ENST00000514600.1 00012 00725 ENST00000441272.2 00013 00265 ENST00000466034.1 00013 00525 ENST00000587085.1 00013 00750 ENST00000399543.1 00013 00230 ENST00000595732.1 00013 00220 ENST00000399152.2 00013 00705 ENST00000414128.1 00014 00215 ENST00000502934.1 00014 00765 ENST00000441053.1 00014 00255 ENST00000422417.1 00014 00253 ENST00000422038.1 00014 00765 ENST00000607723.1 00015 00750 ENST00000503037.1 00015 00195 ENST00000515811.1 00015 00815 ENST00000424215.1 00015 00230 ENST00000482381.1 00015 00240 ENST00000410830.1 00015 00235 ENST00000513572.1 00016 00760 ENST00000594898.1 00016 00783 ENST00000479610.1 00016 00255 ENST00000502861.1 00016 00790 ENST00000455541.1 00016 00205 ENST00000459861.1 00016 00235 ENST00000424592.1 00016 00720 ENST00000424246.1 00017 00750 ENST00000492209.1 00017 00265 ENST00000448134.1 00017 00230 ENST00000510853.2 00017 00240 ENST00000431911.1 00017 00200 ENST00000451711.1 00017 00215 ENST00000452618.1 00017 00705 ENST00000568928.1 00017 00765 ENST00000563320.1 00018 00775 ENST00000437488.1 00018 00240 ENST00000443066.2 00018 00743 ENST00000445791.1 00018 00745 ENST00000457169.1 00018 00685 ENST00000417260.1 00018 00765 ENST00000448977.1 00018 00705 ENST00000509745.1 00019 00230 ENST00000420272.2 00019 00250 ENST00000447761.1 00019 00720 ENST00000449845.1 00019 00220 ENST00000527035.1 00019 00215 ENST00000484765.2 00020 00255 ENST00000428891.1 00020 00240 ENST00000450325.1 00021 00255 ENST00000430542.1 00021 00785 ENST00000522525.1 00021 00735 ENST00000507582.1 00021 00240 ENST00000505877.1 00021 00775 ENST00000602445.1 00022 00525 ENST00000431569.1 00022 00668 ENST00000609450.1 00022 00225 ENST00000501965.2 00022 00710 ENST00000441026.1 00022 00725 ENST00000431500.2 00022 00735 ENST00000432125.2 00022 00765 ENST00000505668.1 00023 00720 ENST00000609549.1 00023 00250 ENST00000505736.1 00023 00755 ENST00000523648.1 00023 00255 ENST00000458254.1 00023 00215 ENST00000508719.1 00023 00750 ENST00000514526.1 00023 00175 ENST00000601486.1 00023 00225 ENST00000461864.1 00023 00755 ENST00000502100.2 00023 00210 ENST00000510946.1 00024 00655 ENST00000417481.1 00024 00255 ENST00000504436.1 00024 00250 ENST00000508352.1 00024 00235 ENST00000509416.1 00024 00780 ENST00000521819.1 00025 00245 ENST00000455929.1 00025 00810 ENST00000507361.1 00025 00250 ENST00000460796.1 00025 00265 ENST00000608774.1 00025 00243 ENST00000449783.1 00025 00735 ENST00000444037.1 00026 00250 ENST00000601586.1 00026 00248 ENST00000508847.1 00026 00255 ENST00000421696.2 00026 00660 ENST00000601500.1 00026 00710 ENST00000432981.1 00027 00200 ENST00000504046.1 00027 00800 ENST00000607662.1 00027 00705 ENST00000487624.1 00027 00720 ENST00000340444.1 00027 00270 ENST00000430048.1 00027 00740 ENST00000453665.1 00028 00280 ENST00000607797.1 00028 00735 ENST00000446139.1 00028 00745 ENST00000589496.2 00028 00745 ENST00000601913.1 00028 00580 ENST00000431557.1 00029 00245 ENST00000439050.1 00029 00750 ENST00000494900.1 00029 00680 ENST00000456687.3 00029 00260 ENST00000505162.1 00029 00725 ENST00000597366.1 00030 00715 ENST00000566366.1 00030 00290 ENST00000434207.1 00030 00715 ENST00000609168.1 00030 00715 ENST00000436488.1 00030 00250 ENST00000506852.1 00031 00700 ENST00000452809.1 00031 00675 ENST00000442410.2 00031 00305 ENST00000609354.1 00031 00725 ENST00000429315.3 00032 00285 ENST00000496488.1 00032 00215 ENST00000421157.1 00032 00735 ENST00000498413.1 00032 00245 ENST00000511693.1 00033 00160 ENST00000602433.1 00033 00775 ENST00000507957.1 00034 00690 ENST00000443562.1 00034 00245 ENST00000577528.1 00034 00250 ENST00000415706.1 00034 00675 ENST00000439964.1 00035 00260 ENST00000503593.1 00035 00675 ENST00000498457.1 00035 00285 ENST00000451992.2 00035 00205 ENST00000608465.1 00035 00740 ENST00000244820.2 00035 00720 ENST00000413304.2 00035 00275 ENST00000515184.1 00035 00260 ENST00000452795.2 00035 00243 ENST00000427213.1 00036 00750 ENST00000424451.1 00036 00665 ENST00000503403.1 00036 00700 ENST00000416506.1 00037 00240 ENST00000432038.1 00037 00255 ENST00000521805.1 00037 00255 ENST00000425914.2 00037 00285 ENST00000604716.1 00037 00260 ENST00000507565.1 00037 00720 ENST00000367716.3 00037 00255 ENST00000514239.1 00037 00270 ENST00000498480.1 00038 00270 ENST00000512435.1 00038 00270 ENST00000455988.1 00038 00660 ENST00000606056.1 00038 00220 ENST00000509057.1 00038 00240 ENST00000608511.1 00038 00240 ENST00000452212.1 00039 00315 ENST00000510302.1 00039 00780 ENST00000511602.1 00039 00695 ENST00000515186.1 00039 00705 ENST00000412092.2 00039 00330 ENST00000413828.2 00039 00280 ENST00000465215.1 00039 00375 ENST00000606582.1 00040 00680 ENST00000417786.1 00040 00275 ENST00000514368.1 00040 00258 ENST00000585826.1 00040 00680 ENST00000441245.1 00041 00295 ENST00000472821.1 00041 00595 ENST00000427439.1 00041 00725 ENST00000588108.1 00041 00210 ENST00000441504.1 00041 00683 ENST00000494582.1 00041 00675 ENST00000506465.1 00041 00280 ENST00000511385.1 00041 00320 ENST00000421640.1 00041 00610 ENST00000437290.2 00042 00255 ENST00000602108.1 00042 00260 ENST00000416349.1 00042 00705 ENST00000445180.2 00042 00235 ENST00000511592.1 00042 00675 ENST00000477246.1 00042 00300 ENST00000512155.1 00042 00310 ENST00000608077.1 00042 00290 ENST00000415629.2 00043 00275 ENST00000424474.2 00043 00280 ENST00000605740.1 00043 00730 ENST00000489690.1 00043 00283 ENST00000607950.1 00043 00285 ENST00000513219.1 00043 00265 ENST00000419614.1 00043 00675 ENST00000413234.1 00043 00285 ENST00000420549.1 00043 00720 ENST00000458698.2 00043 00290 ENST00000482019.1 00043 00310 ENST00000509984.1 00044 00270 ENST00000501927.2 00044 00285 ENST00000439024.1 00044 00658 ENST00000511993.1 00044 00215 ENST00000515128.1 00044 00665 ENST00000604677.1 00044 00665 ENST00000606180.1 00045 00250 ENST00000577914.1 00045 00290 ENST00000440900.1 00045 00690 ENST00000431311.1 00046 00295 ENST00000484076.1 00047 00665 ENST00000451101.1 00047 00265 ENST00000381078.1 00047 00290 ENST00000609423.1 00047 00250 ENST00000513955.1 00048 00730 ENST00000445070.1 00048 00720 ENST00000440574.1 00048 00720 ENST00000435643.1 00048 00260 ENST00000609657.1 00048 00720 ENST00000512464.1 00048 00725 ENST00000411509.1 00048 00635 ENST00000607412.1 00049 00675 ENST00000430520.1 00049 00260 ENST00000512882.2 00049 00665 ENST00000511327.1 00049 00735 ENST00000436885.1 00049 00275 ENST00000604215.1 00049 00685 ENST00000443205.1 00049 00610 ENST00000504869.1 00049 00255 ENST00000587568.1 00050 00690 ENST00000608154.1 00050 00320 ENST00000510570.1 00050 00698 ENST00000451289.1 00050 00720 ENST00000458155.1 00050 00710 ENST00000606186.1 00050 00295 ENST00000413525.1 00050 00650 ENST00000438158.1 00050 00295 ENST00000483840.1 00050 00760 ENST00000604448.1 00051 00725 ENST00000414086.1 00051 00250 ENST00000457440.1 00052 00280 ENST00000503998.1 00052 00720 ENST00000603884.1 00052 00735 ENST00000444649.1 00052 00280 ENST00000504249.1 00052 00280 ENST00000433876.2 00053 00270 ENST00000607946.1 00053 00265 ENST00000508696.1 00053 00708 ENST00000503009.1 00054 00275 ENST00000488287.1 00054 00705 ENST00000504989.1 00055 00295 ENST00000431999.1 00055 00250 ENST00000513871.1 00055 00265 ENST00000450709.1 00055 00255 ENST00000416395.1 00056 00275 ENST00000568817.1 00056 00700 ENST00000437267.2 00056 00245 ENST00000466225.2 00056 00255 ENST00000510230.1 00057 00283 ENST00000453039.1 00057 00780 ENST00000500224.2 00057 00225 ENST00000510198.1 00057 00275 ENST00000515199.1 00058 00700 ENST00000505626.1 00058 00725 ENST00000522350.1 00058 00240 ENST00000507236.1 00058 00265 ENST00000417557.1 00058 00735 ENST00000609881.1 00058 00295 ENST00000458359.1 00059 00270 ENST00000564748.1 00059 00710 ENST00000427892.1 00059 00275 ENST00000511634.1 00059 00285 ENST00000606287.1 00061 00290 ENST00000456469.1 00061 00270 ENST00000418620.1 00062 00265 ENST00000602484.1 00062 00735 ENST00000473713.1 00063 00275 ENST00000503321.1 00064 00290 ENST00000432386.1 00065 00280 ENST00000440358.1 00065 00275 ENST00000440371.1 00066 00290 ENST00000457364.2 00066 00300 ENST00000510349.1 00066 00290 ENST00000528692.1 00067 00295 ENST00000606239.1 00067 00710 ENST00000443928.2 00067 00295 ENST00000453828.1 00067 00300 ENST00000608123.1 00067 00295 ENST00000602434.1 00067 00715 ENST00000441870.1 00067 00295 ENST00000449012.1 00068 00270 ENST00000610235.1 00069 00285 ENST00000427176.1 00070 00295 ENST00000417324.1 00070 00300 ENST00000610094.1 00071 00290 ENST00000594608.1 00071 00300 ENST00000607338.1 00071 00295 ENST00000606696.1 00073 00700 ENST00000513926.1 00073 00285 ENST00000596887.1 00074 00705 ENST00000433084.1 00074 00290 ENST00000600928.1 00074 00240 ENST00000606233.1 00075 00280 ENST00000439795.1 00076 00280 ENST00000310916.3 00076 00710 ENST00000457079.1 00077 00295 ENST00000443093.2 00078 00255 ENST00000443237.1 00078 00300 ENST00000424628.1 00079 00290 ENST00000587162.1 00079 00300 ENST00000609900.1 00080 00705 ENST00000608069.1 00081 00775 ENST00000600062.1 00081 00700 ENST00000566840.1 00081 00295 ENST00000507776.1 00082 00250 ENST00000453732.1 00083 00290 ENST00000452553.1 00083 00295 ENST00000504250.1 00084 00285 ENST00000417926.1 00084 00710 ENST00000512035.1 00084 00285 ENST00000515286.1 00084 00270 ENST00000587306.1 00085 00280 ENST00000557729.1 00086 00245 ENST00000610091.1 00086 00715 ENST00000602919.1 00086 00300 ENST00000441773.1 00086 00295 ENST00000589150.1 00087 00300 ENST00000589487.1 00087 00258 ENST00000503589.1 00087 00280 ENST00000414765.1 00090 00295 ENST00000433186.1 00090 00278 ENST00000427804.1 00091 00295 ENST00000439246.1 00091 00265 ENST00000431268.1 00091 00260 ENST00000510637.1 00091 00745 ENST00000446029.1 00092 00288 ENST00000503488.2 00092 00705 ENST00000462835.1 00093 00285 ENST00000435557.1 00093 00290 ENST00000515405.1 00093 00240 ENST00000423921.1 00093 00190 ENST00000515842.1 00094 00295 ENST00000599448.1 00094 00235 ENST00000605698.1 00095 00300 ENST00000510753.1 00095 00715 ENST00000414634.1 00097 00293 ENST00000517934.1 00098 00270 ENST00000510850.1 00099 00700 ENST00000414688.1 00099 00710 ENST00000273083.3 00099 00290 ENST00000552418.1 00099 00285 ENST00000436248.3 00100 00275 ENST00000439893.1 00102 00250 ENST00000427354.1 00102 00235 ENST00000517299.1 00103 00295 ENST00000569711.1 00104 00280 ENST00000453347.1 00106 00300 ENST00000507373.1 00107 00295 ENST00000453155.1 00108 00295 ENST00000465946.1 00108 00300 ENST00000515086.1 00109 00280 ENST00000449086.1 00110 00745 ENST00000540997.1 00111 00705 ENST00000572124.1 00111 00705 ENST00000508986.1 00120 00288 ENST00000505028.1 00120 00295 ENST00000426444.1 00122 00285 ENST00000507916.2 00124 00700 ENST00000514265.1 00126 00725 ENST00000510632.1 00126 00295 ENST00000597651.1 00127 00295 ENST00000443800.1 00132 00300 ENST00000508255.1 00134 00295 ENST00000607847.1 00137 00705 ENST00000430904.1 00140 00295 ENST00000594622.1 00142 00700 ENST00000436121.1 00144 00710 ENST00000503757.1 00145 00280 ENST00000507011.1 00146 00270 ENST00000609270.1 00146 00735 ENST00000500526.1 00147 00290 ENST00000429230.1 00151 00300 ENST00000601684.1 00155 00290 ENST00000434306.1 00155 00705 ENST00000602820.1 00164 00250 ENST00000425449.1 00168 00730 ENST00000433377.1 00169 00295 ENST00000424528.2 00172 00710 ENST00000597871.1 00176 00300 ENST00000593876.1 00177 00760 ENST00000412674.1 00184 00280 ENST00000432658.1 00195 00718 ENST00000588796.1 00207 00290 ENST00000430540.1 00212 00300 ENST00000565748.1 00215 00715 ENST00000415543.1 00215 00275 ENST00000485338.1 00216 00293 ENST00000436706.1 00232 00300 ENST00000431691.1 00235 00715 ENST00000522762.1 00241 00290 ENST00000506086.2 00254 00300 ENST00000596220.1 00258 00278 ENST00000468859.1 00262 00700 ENST00000511241.1 00268 00290 ENST00000457387.1 00276 00285 ENST00000451707.1 00307 00715 ENST00000524210.1 00317 00720 ENST00000458182.1 00323 00280 ENST00000447880.1 00324 00300 ENST00000508000.1 00380 00720 ENST00000432558.1 00463 00265 ENST00000465347.1 00474 00300 ENST00000514802.1 00571 00295

Comparison Between Low LVEF (LVEF≤45%) and High LVEF (LVEF>45%) at D3-D5 Serum Samples

First, samples are grouped into 2 group by a dichotomized variable: 1-month LVEF<45% and 1-month LVEF>45%.

277 lncRNA are differentially expressed and among these, 70 lncRNA are differentially expressed and have a fold change>2 or <0.5 between the low LVEF (LVEF≤45%) and the high LVEF (LVEF>45%) groups. The p-value and the fold-change of these lncRNA are listed in the Table 36. 369 lncRNAs which have a p<0.05 and/or an individual AUC>0.7 or <0.3 are listed in Table 37.

TABLE 36 List of 70 lncRNA from Gencode database which are differentially expressed (p < 0.05) and have a fold change > 2 or <0.5 between the low LVEF group (LVEF ≤ 45%) and the high LVEF group (LVEF > 45%) p Value Fold change lncRNA p Value Fold change ENST00000437488.1 0.000 0.072 ENST00000452809.1 0.024 2.386 ENST00000507236.1 0.001 0.477 ENST00000509999.1 0.025 2.321 ENST00000505848.1 0.001 0.315 ENST00000515184.1 0.026 0.456 ENST00000509416.1 0.002 2.150 ENST00000517934.1 0.027 0.288 ENST00000451894.2 0.003 2.266 ENST00000590186.1 0.028 0.248 ENST00000477805.1 0.003 0.236 ENST00000510632.1 0.028 0.389 ENST00000562054.1 0.004 0.456 ENST00000429352.1 0.028 0.497 ENST00000502757.1 0.004 2.498 ENST00000514368.1 0.029 0.335 ENST00000609549.1 0.005 0.289 ENST00000451607.1 0.029 0.252 ENST00000519929.1 0.006 0.354 ENST00000435580.1 0.030 0.343 ENST00000515286.1 0.006 0.244 ENST00000429230.1 0.030 0.213 ENST00000427825.1 0.006 0.479 ENST00000426716.1 0.031 3.178 ENST00000457815.1 0.007 2.063 ENST00000510261.1 0.031 4.086 ENST00000512458.1 0.007 0.254 ENST00000599448.1 0.032 0.324 ENST00000514724.2 0.007 0.148 ENST00000436121.1 0.033 2.086 ENST00000513219.1 0.008 0.271 ENST00000600693.1 0.036 0.359 ENST00000456255.1 0.010 0.286 ENST00000521819.1 0.036 0.195 ENST00000503037.1 0.011 0.450 ENST00000508968.1 0.036 0.314 ENST00000427732.1 0.011 4.147 ENST00000598349.1 0.037 2.579 ENST00000506292.2 0.011 0.321 ENST00000453568.1 0.037 0.410 ENST00000357876.5 0.012 0.209 ENST00000443800.1 0.037 0.396 ENST00000588108.1 0.013 0.260 ENST00000435023.1 0.037 0.487 ENST00000514877.1 0.013 0.427 ENST00000431569.1 0.038 3.721 ENST00000426551.1 0.013 0.283 ENST00000439893.1 0.038 0.390 ENST00000440516.1 0.013 2.510 ENST00000508847.1 0.038 0.256 ENST00000422996.1 0.015 0.494 ENST00000587568.1 0.040 3.573 ENST00000587306.1 0.016 0.482 ENST00000418620.1 0.041 0.248 ENST00000439878.1 0.017 0.484 ENST00000509497.1 0.041 0.337 ENST00000506068.1 0.018 3.665 ENST00000527035.1 0.042 0.369 ENST00000431650.1 0.018 0.366 ENST00000498480.1 0.042 0.447 ENST00000421498.1 0.021 3.747 ENST00000415629.2 0.043 0.145 ENST00000507011.1 0.022 0.282 ENST00000514661.1 0.044 2.482 ENST00000507932.1 0.022 0.289 ENST00000465215.1 0.046 0.179 ENST00000515405.1 0.024 0.256 ENST00000416453.2 0.048 2.769 ENST00000432978.1 0.024 0.453 ENST00000505339.1 0.048 3.529

TABLE 37 List of 369 IncRNA from Gencode database which are differentially expressed (p < 0.05) and/or have an AUC >0.7 or <0.3 between the low LVEF group (LVEF ≤ 45%) and the high LVEF group (LVEF > 45%) IncRNA p Value auc ENST00000437488.1 0.000 0.147 ENST00000441790.1 0.000 0.862 ENST00000587085.1 0.000 0.849 ENST00000451711.1 0.001 0.156 ENST00000507236.1 0.001 0.164 ENST00000513955.1 0.001 0.849 ENST00000505848.1 0.001 0.173 ENST00000598757.1 0.001 0.191 ENST00000417926.1 0.001 0.867 ENST00000441053.1 0.001 0.209 ENST00000444037.1 0.002 0.187 ENST00000509416.1 0.002 0.844 ENST00000435552.1 0.002 0.191 ENST00000416930.2 0.002 0.213 ENST00000438158.1 0.003 0.200 ENST00000565044.1 0.003 0.196 ENST00000451894.2 0.003 0.796 ENST00000477805.1 0.003 0.222 ENST00000450713.1 0.003 0.800 ENST00000562054.1 0.004 0.191 ENST00000412228.1 0.004 0.227 ENST00000417324.1 0.004 0.209 ENST00000513767.3 0.004 0.178 ENST00000502757.1 0.004 0.804 ENST00000608574.1 0.004 0.200 ENST00000456026.1 0.005 0.756 ENST00000609549.1 0.005 0.276 ENST00000608077.1 0.005 0.253 ENST00000589496.2 0.005 0.782 ENST00000568384.1 0.005 0.213 ENST00000440371.1 0.005 0.236 ENST00000366187.2 0.005 0.791 ENST00000607068.1 0.006 0.213 ENST00000519929.1 0.006 0.213 ENST00000504246.1 0.006 0.209 ENST00000515286.1 0.006 0.218 ENST00000427825.1 0.006 0.236 ENST00000412294.1 0.006 0.778 ENST00000512882.2 0.007 0.791 ENST00000424246.1 0.007 0.769 ENST00000457815.1 0.007 0.769 ENST00000512458.1 0.007 0.251 ENST00000510795.1 0.007 0.791 ENST00000422038.1 0.007 0.756 ENST00000428156.1 0.007 0.813 ENST00000514724.2 0.007 0.267 ENST00000418602.1 0.008 0.244 ENST00000506892.1 0.008 0.258 ENST00000513219.1 0.008 0.240 ENST00000420365.1 0.008 0.249 ENST00000602528.1 0.009 0.778 ENST00000430666.1 0.009 0.218 ENST00000508486.2 0.009 0.773 ENST00000607216.1 0.010 0.227 ENST00000456255.1 0.010 0.233 ENST00000424895.1 0.011 0.747 ENST00000565428.1 0.011 0.258 ENST00000503037.1 0.011 0.240 ENST00000503929.1 0.011 0.773 ENST00000427732.1 0.011 0.769 ENST00000427804.1 0.011 0.209 ENST00000506292.2 0.011 0.244 ENST00000452738.1 0.011 0.738 ENST00000420549.1 0.012 0.804 ENST00000445523.1 0.012 0.769 ENST00000357876.5 0.012 0.249 ENST00000513572.1 0.012 0.751 ENST00000443613.2 0.012 0.240 ENST00000600062.1 0.012 0.764 ENST00000479610.1 0.012 0.267 ENST00000588108.1 0.013 0.200 ENST00000446139.1 0.013 0.791 ENST00000510381.2 0.013 0.773 ENST00000514877.1 0.013 0.233 ENST00000426551.1 0.013 0.284 ENST00000507361.1 0.013 0.244 ENST00000504046.1 0.013 0.769 ENST00000462431.1 0.013 0.787 ENST00000491676.1 0.013 0.244 ENST00000440516.1 0.013 0.764 ENST00000609900.1 0.014 0.800 ENST00000589150.1 0.014 0.258 ENST00000596829.1 0.014 0.227 ENST00000601955.1 0.014 0.271 ENST00000608482.1 0.015 0.244 ENST00000457489.1 0.015 0.747 ENST00000422996.1 0.015 0.249 ENST00000495228.1 0.015 0.253 ENST00000477539.2 0.016 0.756 ENST00000503616.1 0.016 0.262 ENST00000587306.1 0.016 0.244 ENST00000608123.1 0.016 0.267 ENST00000439878.1 0.017 0.238 ENST00000607002.1 0.017 0.249 ENST00000466291.1 0.017 0.747 ENST00000424244.1 0.018 0.253 ENST00000455929.1 0.018 0.796 ENST00000512417.1 0.018 0.284 ENST00000506068.1 0.018 0.769 ENST00000431650.1 0.018 0.276 ENST00000607723.1 0.018 0.773 ENST00000417765.1 0.019 0.742 ENST00000607540.1 0.019 0.747 ENST00000502467.1 0.019 0.693 ENST00000589024.1 0.019 0.738 ENST00000433219.1 0.019 0.276 ENST00000426881.2 0.019 0.258 ENST00000443928.2 0.019 0.244 ENST00000567904.1 0.020 0.258 ENST00000439479.1 0.020 0.276 ENST00000473001.1 0.020 0.276 ENST00000429666.1 0.020 0.247 ENST00000421498.1 0.021 0.676 ENST00000455038.1 0.021 0.280 ENST00000433175.2 0.022 0.267 ENST00000451101.1 0.022 0.267 ENST00000608777.1 0.022 0.267 ENST00000602919.1 0.022 0.253 ENST00000507011.1 0.022 0.242 ENST00000360083.3 0.022 0.760 ENST00000420272.2 0.022 0.280 ENST00000507932.1 0.022 0.298 ENST00000417644.1 0.023 0.258 ENST00000450746.1 0.023 0.707 ENST00000456687.3 0.023 0.267 ENST00000609354.1 0.024 0.716 ENST00000515405.1 0.024 0.249 ENST00000432978.1 0.024 0.258 ENST00000452809.1 0.024 0.698 ENST00000417795.1 0.025 0.284 ENST00000509999.1 0.025 0.713 ENST00000553319.1 0.025 0.276 ENST00000441272.2 0.025 0.271 ENST00000445180.2 0.026 0.284 ENST00000452840.1 0.026 0.724 ENST00000515153.1 0.026 0.244 ENST00000606696.1 0.026 0.733 ENST00000515184.1 0.026 0.280 ENST00000596887.1 0.027 0.769 ENST00000450944.1 0.027 0.271 ENST00000510935.1 0.027 0.284 ENST00000565538.1 0.027 0.800 ENST00000517934.1 0.027 0.284 ENST00000569860.1 0.027 0.742 ENST00000415628.1 0.027 0.293 ENST00000607831.1 0.027 0.258 ENST00000594798.1 0.027 0.271 ENST00000497573.1 0.028 0.253 ENST00000416689.1 0.028 0.249 ENST00000507424.1 0.028 0.293 ENST00000566527.1 0.028 0.720 ENST00000590186.1 0.028 0.236 ENST00000510632.1 0.028 0.298 ENST00000429352.1 0.028 0.280 ENST00000510175.1 0.029 0.738 ENST00000514368.1 0.029 0.304 ENST00000451607.1 0.029 0.244 ENST00000448786.1 0.030 0.700 ENST00000435580.1 0.030 0.320 ENST00000429230.1 0.030 0.236 ENST00000508752.1 0.030 0.707 ENST00000426716.1 0.031 0.713 ENST00000423600.1 0.031 0.271 ENST00000417976.1 0.031 0.707 ENST00000510261.1 0.031 0.711 ENST00000442864.1 0.031 0.698 ENST00000442956.1 0.031 0.276 ENST00000458698.2 0.031 0.284 ENST00000506305.1 0.032 0.280 ENST00000599448.1 0.032 0.258 ENST00000505347.1 0.032 0.293 ENST00000436121.1 0.033 0.760 ENST00000606217.1 0.033 0.284 ENST00000608360.1 0.033 0.298 ENST00000439024.1 0.033 0.667 ENST00000414030.1 0.033 0.276 ENST00000437798.1 0.034 0.329 ENST00000449845.1 0.034 0.284 ENST00000566840.1 0.034 0.262 ENST00000460574.1 0.034 0.280 ENST00000438553.1 0.034 0.729 ENST00000605571.1 0.034 0.267 ENST00000439186.1 0.034 0.727 ENST00000412369.1 0.034 0.298 ENST00000412483.1 0.035 0.262 ENST00000607830.1 0.035 0.284 ENST00000505348.1 0.035 0.729 ENST00000600693.1 0.036 0.267 ENST00000438002.1 0.036 0.293 ENST00000431435.1 0.036 0.716 ENST00000521819.1 0.036 0.331 ENST00000569502.1 0.036 0.293 ENST00000508968.1 0.036 0.287 ENST00000413304.2 0.037 0.320 ENST00000562952.1 0.037 0.724 ENST00000598349.1 0.037 0.649 ENST00000453568.1 0.037 0.280 ENST00000482019.1 0.037 0.324 ENST00000418244.1 0.037 0.269 ENST00000443800.1 0.037 0.271 ENST00000435023.1 0.037 0.307 ENST00000440545.1 0.037 0.724 ENST00000452509.1 0.037 0.724 ENST00000431569.1 0.038 0.611 ENST00000439893.1 0.038 0.187 ENST00000508847.1 0.038 0.311 ENST00000453128.1 0.039 0.267 ENST00000458254.1 0.039 0.267 ENST00000594189.1 0.039 0.253 ENST00000502934.1 0.040 0.711 ENST00000587568.1 0.040 0.720 ENST00000431985.1 0.040 0.302 ENST00000507344.1 0.040 0.738 ENST00000471990.2 0.041 0.702 ENST00000597543.1 0.041 0.702 ENST00000418620.1 0.041 0.302 ENST00000443205.1 0.041 0.684 ENST00000483840.1 0.041 0.716 ENST00000509497.1 0.041 0.302 ENST00000412134.1 0.042 0.742 ENST00000511517.1 0.042 0.311 ENST00000503267.1 0.042 0.311 ENST00000607662.1 0.042 0.724 ENST00000507517.1 0.042 0.307 ENST00000527035.1 0.042 0.282 ENST00000498480.1 0.042 0.276 ENST00000507251.1 0.042 0.711 ENST00000417651.1 0.042 0.280 ENST00000415629.2 0.043 0.333 ENST00000417805.1 0.043 0.711 ENST00000606069.1 0.043 0.298 ENST00000431362.1 0.043 0.253 ENST00000610091.1 0.043 0.729 ENST00000515422.1 0.044 0.698 ENST00000514661.1 0.044 0.644 ENST00000608605.1 0.044 0.311 ENST00000414625.2 0.044 0.316 ENST00000514600.1 0.044 0.787 ENST00000416209.2 0.044 0.293 ENST00000597366.1 0.044 0.707 ENST00000417695.1 0.044 0.293 ENST00000448901.1 0.044 0.760 ENST00000424612.1 0.045 0.311 ENST00000606287.1 0.045 0.289 ENST00000607594.1 0.045 0.689 ENST00000367716.3 0.045 0.293 ENST00000607541.1 0.045 0.293 ENST00000432386.1 0.045 0.298 ENST00000508799.1 0.045 0.284 ENST00000605698.1 0.045 0.311 ENST00000399543.1 0.045 0.262 ENST00000513540.1 0.045 0.733 ENST00000427819.1 0.046 0.716 ENST00000509548.2 0.046 0.676 ENST00000424689.1 0.046 0.298 ENST00000465215.1 0.046 0.458 ENST00000512637.1 0.046 0.311 ENST00000436207.2 0.046 0.771 ENST00000508696.1 0.046 0.711 ENST00000609881.1 0.046 0.298 ENST00000515243.1 0.046 0.276 ENST00000438414.1 0.047 0.338 ENST00000458007.2 0.047 0.271 ENST00000424748.1 0.047 0.293 ENST00000508959.1 0.047 0.302 ENST00000596329.1 0.047 0.364 ENST00000446521.1 0.048 0.284 ENST00000512965.1 0.048 0.704 ENST00000416453.2 0.048 0.658 ENST00000505339.1 0.048 0.578 ENST00000417563.1 0.049 0.713 ENST00000440322.1 0.049 0.716 ENST00000596632.1 0.049 0.298 ENST00000451289.1 0.049 0.716 ENST00000437267.2 0.049 0.276 ENST00000520443.1 0.049 0.671 ENST00000523648.1 0.049 0.316 ENST00000449140.2 0.049 0.284 ENST00000594351.1 0.051 0.293 ENST00000506660.1 0.051 0.293 ENST00000608881.1 0.051 0.711 ENST00000463978.1 0.051 0.720 ENST00000507782.1 0.051 0.293 ENST00000436475.2 0.051 0.720 ENST00000512464.1 0.052 0.720 ENST00000599387.1 0.052 0.702 ENST00000441587.2 0.052 0.716 ENST00000504765.1 0.052 0.716 ENST00000430542.1 0.053 0.720 ENST00000549744.1 0.053 0.284 ENST00000441459.1 0.053 0.298 ENST00000453988.1 0.055 0.249 ENST00000414634.1 0.056 0.278 ENST00000515842.1 0.056 0.289 ENST00000456897.1 0.057 0.284 ENST00000449673.1 0.057 0.276 ENST00000511091.1 0.057 0.702 ENST00000449783.1 0.057 0.733 ENST00000414938.1 0.058 0.253 ENST00000515811.1 0.058 0.716 ENST00000589853.1 0.060 0.711 ENST00000476125.1 0.061 0.707 ENST00000451992.2 0.062 0.262 ENST00000562191.1 0.062 0.724 ENST00000505572.1 0.062 0.716 ENST00000434572.1 0.062 0.262 ENST00000454348.1 0.064 0.271 ENST00000482609.1 0.064 0.262 ENST00000511241.1 0.064 0.213 ENST00000504263.1 0.070 0.716 ENST00000418925.1 0.071 0.298 ENST00000417482.1 0.071 0.271 ENST00000514265.1 0.072 0.742 ENST00000467438.1 0.072 0.244 ENST00000608069.1 0.073 0.711 ENST00000587696.1 0.076 0.293 ENST00000609583.1 0.076 0.300 ENST00000446411.1 0.076 0.738 ENST00000443093.2 0.077 0.253 ENST00000431759.1 0.077 0.289 ENST00000418387.1 0.078 0.733 ENST00000419609.1 0.079 0.716 ENST00000466225.2 0.079 0.280 ENST00000513926.1 0.081 0.298 ENST00000437631.1 0.082 0.760 ENST00000430520.1 0.082 0.296 ENST00000506852.1 0.084 0.751 ENST00000510753.1 0.085 0.707 ENST00000447389.1 0.089 0.716 ENST00000436262.1 0.091 0.271 ENST00000496242.1 0.091 0.280 ENST00000453324.1 0.092 0.280 ENST00000602108.1 0.096 0.267 ENST00000505538.1 0.099 0.298 ENST00000606056.1 0.101 0.280 ENST00000508719.1 0.102 0.702 ENST00000512370.1 0.107 0.271 ENST00000427421.1 0.107 0.293 ENST00000609097.1 0.108 0.711 ENST00000602433.1 0.116 0.720 ENST00000512090.1 0.117 0.298 ENST00000588944.1 0.118 0.702 ENST00000426519.1 0.119 0.716 ENST00000506454.1 0.121 0.720 ENST00000515337.1 0.126 0.271 ENST00000505371.2 0.127 0.296 ENST00000503685.1 0.131 0.289 ENST00000503163.1 0.132 0.271 ENST00000504829.1 0.136 0.707 ENST00000431856.1 0.136 0.716 ENST00000607164.1 0.138 0.738 ENST00000503113.1 0.141 0.293 ENST00000503320.1 0.150 0.298 ENST00000356684.3 0.156 0.702 ENST00000565748.1 0.156 0.702 ENST00000423921.1 0.158 0.276 ENST00000462835.1 0.158 0.289 ENST00000512185.1 0.158 0.298 ENST00000513591.1 0.162 0.298 ENST00000366278.2 0.165 0.711 ENST00000505018.1 0.166 0.760 ENST00000453370.1 0.166 0.716 ENST00000502100.2 0.178 0.289 ENST00000416221.1 0.190 0.720 ENST00000596220.1 0.195 0.267 ENST00000593876.1 0.291 0.742 ENST00000602972.1 0.335 0.284 ENST00000456146.1 0.346 0.718 ENST00000607769.1 0.539 0.293

Comparison Between Low LVEF (LVEF≤40%) and High LVEF (LVEF>40%) at D0 in Serum Samples of AMI Patients

First, samples are grouped into 2 groups by a dichotomized variable: 1-month LVEF<40% and 1-month LVEF>40%.

273 lncRNA are differentially expressed and among these, 83 lncRNA are differentially expressed and have a fold change>2 or <0.5 between the low LVEF (LVEF≤40%) and the high LVEF (LVEF>40%). 3 lncRNAs are common to D3 samples (ENST00000421563.1, ENST00000443562.1, ENST00000455988.1). The p-value and the fold-change of these lncRNA are listed in the Table 38. In Table 39, 235 lncRNAs which have a p<0.05 and an individual AUC>0.7 or <0.3 are listed in Table 39.

TABLE 38 List of 83 lncRNA from Gencode database which are differentially expressed (p < 0.05) and have a fold change > 2 or <0.5 between the low LVEF group (LVEF ≤ 40%) and the high LVEF group (LVEF > 40%) lncRNA p Value fold change ENST00000510165.1 0.000 0.454 ENST00000449154.1 0.001 3.668 ENST00000523354.1 0.001 2.383 ENST00000598798.1 0.001 3.678 ENST00000421563.1 0.001 2.688 ENST00000513851.1 0.002 2.445 ENST00000515842.1 0.002 0.453 ENST00000508845.1 0.004 2.084 ENST00000506338.1 0.004 3.476 ENST00000453015.1 0.006 0.491 ENST00000505997.1 0.006 12.552 ENST00000507435.1 0.007 4.142 ENST00000504368.1 0.007 2.362 ENST00000420672.1 0.008 7.02E+28 ENST00000504165.1 0.008 2.796 ENST00000412311.1 0.009 6.569 ENST00000454183.1 0.009 4.501 ENST00000422253.1 0.010 3.571 ENST00000490497.1 0.011 6.17E+13 ENST00000402410.2 0.011 9.911 ENST00000513660.2 0.012 3.751 ENST00000511222.1 0.012 2.305 ENST00000439239.2 0.013 2.069 ENST00000549878.1 0.013 2.466 ENST00000444217.1 0.013 2.075 ENST00000435548.1 0.014 5.647 ENST00000607026.1 0.014 0.480 ENST00000515111.1 0.048 2.667 ENST00000503093.1 0.014 4.916 ENST00000443670.1 0.014 2.095 ENST00000429608.1 0.015 2.188 ENST00000518276.1 0.016 2.734 ENST00000420418.1 0.016 4.067 ENST00000511419.1 0.017 3.308 ENST00000431130.2 0.017 2.765 ENST00000412171.2 0.020 988.115 ENST00000419531.2 0.021 0.003 ENST00000442384.1 0.022 2.042 ENST00000446102.1 0.022 0.481 ENST00000414102.1 0.022 0.365 ENST00000507963.1 0.022 4.620 ENST00000609843.1 0.024 2.273 ENST00000449124.1 0.025 3.322 ENST00000425192.1 0.025 2.64E+12 ENST00000514377.1 0.025 4.851 ENST00000515680.2 0.027 2.330 ENST00000423168.1 0.028 4.270 ENST00000429230.1 0.028 3.757 ENST00000604660.1 0.029 2.349 ENST00000421298.1 0.029 3.474 ENST00000492209.1 0.030 2.082 ENST00000523311.1 0.031 2.078 ENST00000434796.1 0.031 2.290 ENST00000447876.1 0.031 0.287 ENST00000576302.1 0.032 3.094 ENST00000457686.1 0.049 0.231 ENST00000588145.1 0.032 13.047 ENST00000602470.1 0.032 2.968 ENST00000497379.2 0.033 0.330 ENST00000506100.1 0.033 2.451 ENST00000609352.1 0.034 2.228 ENST00000507476.1 0.034 3.547 ENST00000415202.1 0.035 6.887 ENST00000599781.1 0.036 0.075 ENST00000497551.2 0.037 2.235 ENST00000597654.1 0.037 0.037 ENST00000439606.1 0.038 7.846 ENST00000455988.1 0.038 2.302 ENST00000597904.1 0.039 2.634 ENST00000505972.2 0.039 0.466 ENST00000609140.1 0.040 68.930 ENST00000443284.1 0.041 2.225 ENST00000502812.2 0.042 0.359 ENST00000552026.1 0.043 2.692 ENST00000522300.1 0.043 0.468 ENST00000440038.2 0.044 7.706 ENST00000413841.1 0.044 2.153 ENST00000443562.1 0.044 2.013 ENST00000457941.1 0.045 17.472 ENST00000605147.1 0.046 0.409 ENST00000456803.1 0.047 0.465 ENST00000578974.2 0.048 0.387 ENST00000509212.1 0.048 0.492

TABLE 39 List of 235 IncRNA from Gencode database, which are differentially expressed (p < 0.05) and have an AUC >0.7 or <0.3 between the low LVEF group (LVEF ≤ 40%) and the high LVEF group (LVEF > 40%) IncRNA p Value auc ENST00000510165.1 0.000 0.034 ENST00000431244.1 0.001 0.085 ENST00000449154.1 0.001 0.868 ENST00000414199.1 0.001 0.880 ENST00000523354.1 0.001 0.829 ENST00000454595.1 0.001 0.863 ENST00000598798.1 0.001 0.859 ENST00000421563.1 0.001 0.872 ENST00000417926.1 0.001 0.863 ENST00000513851.1 0.002 0.863 ENST00000515842.1 0.002 0.094 ENST00000444672.1 0.002 0.880 ENST00000420071.1 0.002 0.880 ENST00000420350.1 0.002 0.128 ENST00000512417.1 0.003 0.855 ENST00000608111.1 0.004 0.846 ENST00000508845.1 0.004 0.829 ENST00000506338.1 0.004 0.803 ENST00000430897.1 0.004 0.162 ENST00000601136.1 0.005 0.872 ENST00000430520.1 0.005 0.137 ENST00000522312.1 0.005 0.137 ENST00000451396.2 0.005 0.838 ENST00000453015.1 0.006 0.179 ENST00000397645.2 0.006 0.838 ENST00000449586.1 0.006 0.821 ENST00000356684.3 0.006 0.162 ENST00000505997.1 0.006 0.761 ENST00000508619.1 0.007 0.829 ENST00000507435.1 0.007 0.786 ENST00000510254.1 0.007 0.197 ENST00000440104.1 0.007 0.829 ENST00000504368.1 0.007 0.786 ENST00000438506.1 0.008 0.829 ENST00000420672.1 0.008 0.859 ENST00000412313.1 0.008 0.128 ENST00000504165.1 0.008 0.803 ENST00000511234.1 0.008 0.179 ENST00000510879.1 0.009 0.872 ENST00000412311.1 0.009 0.722 ENST00000439795.1 0.009 0.222 ENST00000434094.1 0.009 0.179 ENST00000454183.1 0.009 0.774 ENST00000504207.1 0.009 0.179 ENST00000504297.1 0.010 0.846 ENST00000503568.1 0.010 0.821 ENST00000412357.1 0.010 0.803 ENST00000460597.1 0.010 0.821 ENST00000422253.1 0.010 0.803 ENST00000506655.1 0.011 0.812 ENST00000526176.1 0.011 0.821 ENST00000402410.2 0.011 0.761 ENST00000455121.3 0.012 0.162 ENST00000513660.2 0.012 0.769 ENST00000602411.1 0.012 0.778 ENST00000511222.1 0.012 0.752 ENST00000607594.1 0.013 0.812 ENST00000450500.1 0.013 0.786 ENST00000439239.2 0.013 0.795 ENST00000549878.1 0.013 0.761 ENST00000418015.1 0.013 0.821 ENST00000444217.1 0.013 0.786 ENST00000435548.1 0.014 0.795 ENST00000607026.1 0.014 0.188 ENST00000503093.1 0.014 0.739 ENST00000509184.1 0.014 0.821 ENST00000443670.1 0.014 0.769 ENST00000486767.1 0.015 0.786 ENST00000457402.1 0.015 0.188 ENST00000515789.1 0.015 0.197 ENST00000429608.1 0.015 0.782 ENST00000592182.1 0.016 0.786 ENST00000422259.1 0.016 0.231 ENST00000442200.1 0.016 0.786 ENST00000432733.1 0.016 0.214 ENST00000518276.1 0.016 0.744 ENST00000420418.1 0.016 0.761 ENST00000297163.3 0.016 0.744 ENST00000453155.1 0.016 0.821 ENST00000496154.2 0.017 0.179 ENST00000511419.1 0.017 0.761 ENST00000431130.2 0.017 0.765 ENST00000487657.2 0.017 0.786 ENST00000514241.1 0.017 0.214 ENST00000604571.1 0.017 0.162 ENST00000428624.1 0.018 0.162 ENST00000592948.1 0.018 0.222 ENST00000418335.1 0.018 0.171 ENST00000435895.1 0.018 0.171 ENST00000322353.3 0.019 0.744 ENST00000512464.1 0.019 0.803 ENST00000448713.1 0.019 0.778 ENST00000467240.1 0.019 0.786 ENST00000444647.1 0.019 0.239 ENST00000425974.1 0.020 0.769 ENST00000452176.1 0.020 0.778 ENST00000510416.1 0.020 0.761 ENST00000503188.1 0.020 0.197 ENST00000509559.1 0.021 0.188 ENST00000508255.1 0.021 0.214 ENST00000419531.2 0.021 0.128 ENST00000430471.1 0.021 0.786 ENST00000442384.1 0.022 0.761 ENST00000446102.1 0.022 0.188 ENST00000414102.1 0.022 0.179 ENST00000428651.1 0.022 0.231 ENST00000507963.1 0.022 0.726 ENST00000473595.1 0.023 0.761 ENST00000326734.1 0.023 0.256 ENST00000435692.2 0.023 0.863 ENST00000513812.1 0.023 0.726 ENST00000609843.1 0.024 0.752 ENST00000449124.1 0.025 0.795 ENST00000433108.1 0.025 0.778 ENST00000425192.1 0.025 0.726 ENST00000514377.1 0.025 0.752 ENST00000444346.1 0.025 0.239 ENST00000513770.1 0.026 0.778 ENST00000448431.1 0.026 0.214 ENST00000440404.1 0.026 0.197 ENST00000560688.1 0.026 0.248 ENST00000428176.1 0.026 0.248 ENST00000515680.2 0.027 0.765 ENST00000446136.1 0.027 0.769 ENST00000511279.1 0.028 0.752 ENST00000423168.1 0.028 0.838 ENST00000429230.1 0.028 0.744 ENST00000421437.1 0.029 0.265 ENST00000504728.1 0.029 0.752 ENST00000569928.1 0.029 0.239 ENST00000421298.1 0.029 0.778 ENST00000445565.1 0.030 0.769 ENST00000598710.1 0.030 0.231 ENST00000492209.1 0.030 0.786 ENST00000492300.1 0.030 0.735 ENST00000508484.1 0.030 0.248 ENST00000415174.1 0.030 0.188 ENST00000432505.1 0.031 0.761 ENST00000523311.1 0.031 0.756 ENST00000434796.1 0.031 0.735 ENST00000440266.2 0.031 0.778 ENST00000447876.1 0.031 0.239 ENST00000506070.1 0.031 0.274 ENST00000426083.1 0.032 0.248 ENST00000576302.1 0.032 0.761 ENST00000607950.1 0.032 0.778 ENST00000588145.1 0.032 0.701 ENST00000503259.1 0.032 0.761 ENST00000454380.1 0.032 0.205 ENST00000608925.1 0.032 0.239 ENST00000608442.1 0.032 0.214 ENST00000602470.1 0.032 0.739 ENST00000514011.1 0.033 0.239 ENST00000605589.1 0.033 0.735 ENST00000497379.2 0.033 0.171 ENST00000609352.1 0.034 0.752 ENST00000507476.1 0.034 0.726 ENST00000608777.1 0.035 0.231 ENST00000499292.2 0.035 0.162 ENST00000415202.1 0.035 0.821 ENST00000610144.1 0.035 0.231 ENST00000515188.1 0.035 0.778 ENST00000599781.1 0.036 0.111 ENST00000497551.2 0.037 0.726 ENST00000597654.1 0.037 0.188 ENST00000505364.1 0.037 0.744 ENST00000514427.1 0.038 0.265 ENST00000604680.1 0.038 0.752 ENST00000512546.1 0.038 0.239 ENST00000455988.1 0.038 0.786 ENST00000597904.1 0.039 0.752 ENST00000505972.2 0.039 0.248 ENST00000512873.1 0.039 0.761 ENST00000607459.1 0.039 0.231 ENST00000584829.1 0.039 0.744 ENST00000471626.1 0.039 0.718 ENST00000514265.1 0.039 0.231 ENST00000451362.1 0.039 0.265 ENST00000595232.1 0.039 0.214 ENST00000473798.1 0.039 0.769 ENST00000427748.1 0.040 0.239 ENST00000607389.1 0.040 0.769 ENST00000602316.1 0.040 0.197 ENST00000439601.1 0.040 0.205 ENST00000462176.2 0.040 0.248 ENST00000512519.1 0.040 0.197 ENST00000609140.1 0.040 0.752 ENST00000512527.1 0.041 0.239 ENST00000514010.1 0.041 0.726 ENST00000444043.2 0.041 0.726 ENST00000429871.1 0.041 0.291 ENST00000443284.1 0.041 0.795 ENST00000461448.1 0.041 0.231 ENST00000609969.1 0.041 0.769 ENST00000458097.1 0.041 0.222 ENST00000446073.1 0.042 0.769 ENST00000431691.1 0.042 0.752 ENST00000502812.2 0.042 0.239 ENST00000508470.1 0.043 0.761 ENST00000552026.1 0.043 0.735 ENST00000458007.2 0.043 0.256 ENST00000522300.1 0.043 0.248 ENST00000366441.2 0.043 0.795 ENST00000429269.1 0.043 0.778 ENST00000595268.1 0.044 0.744 ENST00000440038.2 0.044 0.778 ENST00000413841.1 0.044 0.752 ENST00000489011.1 0.044 0.735 ENST00000443562.1 0.044 0.795 ENST00000512349.1 0.045 0.231 ENST00000505736.1 0.045 0.231 ENST00000442020.1 0.045 0.761 ENST00000440862.1 0.045 0.205 ENST00000464242.1 0.045 0.718 ENST00000499900.2 0.045 0.231 ENST00000457941.1 0.045 0.718 ENST00000470263.1 0.045 0.761 ENST00000512581.1 0.045 0.735 ENST00000464428.2 0.045 0.752 ENST00000523745.1 0.046 0.222 ENST00000522173.1 0.046 0.214 ENST00000585718.1 0.046 0.248 ENST00000605147.1 0.046 0.188 ENST00000509496.1 0.047 0.735 ENST00000449298.1 0.047 0.769 ENST00000456803.1 0.047 0.226 ENST00000509212.1 0.048 0.256 ENST00000442036.1 0.048 0.735 ENST00000564300.1 0.048 0.239 ENST00000426504.1 0.048 0.231 ENST00000457686.1 0.049 0.205 ENST00000515542.1 0.049 0.735 ENST00000429469.1 0.050 0.701 ENST00000443008.1 0.050 0.265 ENST00000427524.1 0.034 0.778

Comparison Between Low LVEF (LVEF≤45%) and High LVEF (LVEF>45%) at D0 in Serum Samples of AMI Patients

First, samples are grouped into 2 groups by a dichotomized variable: 1-month LVEF<45% and 1-month LVEF>45%.

243 lncRNA are differentially expressed and among these, 69 lncRNA are differentially expressed and have a fold change>2 or <0.5 between the low LVEF (LVEF≤45%) and the high LVEF (LVEF>45%). 2 lncRNAs are common to D3 samples (ENST00000429230.1, ENST00000599448.1). The p-value and the fold-change of these lncRNA are listed in the Table 40. 211 lncRNAs which have a p<0.05 and an individual AUC>0.7 or <0.3 are listed in Table 41.

TABLE 40 List of 76 lncRNA from Gencode database which are differentially expressed (p < 0.05) and have a fold change > 2 or <0.5 between the low LVEF group (LVEF ≤ 45%) and the high LVEF group (LVEF > 45%) lncRNA p Value foldchange ENST00000449154.1 0.000 3.558 ENST00000523354.1 0.000 2.334 ENST00000453015.1 0.000 0.356 ENST00000435895.1 0.000 0.486 ENST00000552026.1 0.001 3.770 ENST00000415543.1 0.001 0.237 ENST00000436488.1 0.001 0.431 ENST00000599448.1 0.003 0.203 ENST00000441345.2 0.005 0.117 ENST00000430555.1 0.005 2.363 ENST00000608111.1 0.006 17.287 ENST00000607026.1 0.006 0.439 ENST00000435643.1 0.006 0.249 ENST00000597904.1 0.006 3.537 ENST00000496733.2 0.007 0.488 ENST00000607985.1 0.007 0.109 ENST00000465283.1 0.007 0.082 ENST00000429230.1 0.008 4.740 ENST00000443562.1 0.008 2.248 ENST00000461448.1 0.010 0.467 ENST00000507698.1 0.010 2.574 ENST00000594976.1 0.011 0.206 ENST00000606468.1 0.011 2.875 ENST00000431130.2 0.011 2.733 ENST00000605147.1 0.012 0.351 ENST00000469289.1 0.013 5.727 ENST00000427042.1 0.013 2.802 ENST00000413525.1 0.013 0.248 ENST00000461864.1 0.014 0.440 ENST00000439745.1 0.016 0.470 ENST00000402410.2 0.017 6.982 ENST00000507476.1 0.017 4.500 ENST00000421563.1 0.018 2.113 ENST00000515263.1 0.019 0.304 ENST00000433475.1 0.019 9.721 ENST00000436293.2 0.021 4.454 ENST00000509057.1 0.022 2.111 ENST00000457686.1 0.023 0.198 ENST00000523895.1 0.024 0.435 ENST00000419531.2 0.025 0.000 ENST00000444361.1 0.025 0.254 ENST00000601854.1 0.026 5.663 ENST00000441036.1 0.026 2.509 ENST00000505149.1 0.027 0.448 ENST00000435492.1 0.030 0.316 ENST00000512401.1 0.031 0.057 ENST00000507842.1 0.032 2.843 ENST00000510648.1 0.032 3.873 ENST00000606314.1 0.033 3.833 ENST00000474250.1 0.034 4.009 ENST00000509105.1 0.034 8.823 ENST00000588145.1 0.035 13.232 ENST00000470860.1 0.035 0.238 ENST00000485020.1 0.037 0.412 ENST00000447876.1 0.037 0.323 ENST00000426892.1 0.037 2.191 ENST00000512603.1 0.039 0.433 ENST00000602528.1 0.040 0.441 ENST00000424788.1 0.040 0.169 ENST00000424084.1 0.044 6.957 ENST00000507639.1 0.044 3.312 ENST00000426178.1 0.044 0.170 ENST00000417516.1 0.044 2.784 ENST00000416279.1 0.044 2.637 ENST00000443270.1 0.044 3.375 ENST00000469846.2 0.045 0.256 ENST00000508998.1 0.047 3.937 ENST00000598740.1 0.047 2.006 ENST00000597654.1 0.047 0.068

TABLE 41 List of 211 IncRNA from Gencode database, which are differentially expressed (p < 0.05) and have an AUC >0.7 or <0.3 between the low LVEF group (LVEF ≤ 45%) and the high LVEF group (LVEF > 45%) IncRNA p Value auc ENST00000449154.1 0.000 0.923 ENST00000523354.1 0.000 0.897 ENST00000453015.1 0.000 0.068 ENST00000435895.1 0.000 0.068 ENST00000552026.1 0.001 0.889 ENST00000415543.1 0.001 0.128 ENST00000436488.1 0.001 0.103 ENST00000492300.1 0.002 0.872 ENST00000506655.1 0.002 0.872 ENST00000588227.1 0.002 0.838 ENST00000432210.1 0.002 0.889 ENST00000442020.1 0.002 0.872 ENST00000414065.1 0.002 0.829 ENST00000599448.1 0.003 0.188 ENST00000496154.2 0.004 0.137 ENST00000444672.1 0.004 0.872 ENST00000440786.1 0.005 0.829 ENST00000356133.3 0.005 0.855 ENST00000514010.1 0.005 0.855 ENST00000441345.2 0.005 0.111 ENST00000603264.1 0.005 0.162 ENST00000602433.1 0.005 0.205 ENST00000430555.1 0.005 0.846 ENST00000428083.1 0.006 0.838 ENST00000608111.1 0.006 0.915 ENST00000607026.1 0.006 0.248 ENST00000435643.1 0.006 0.188 ENST00000597904.1 0.006 0.880 ENST00000496733.2 0.007 0.188 ENST00000446520.1 0.007 0.188 ENST00000607985.1 0.007 0.235 ENST00000465283.1 0.007 0.261 ENST00000421933.1 0.007 0.162 ENST00000499346.2 0.007 0.812 ENST00000429230.1 0.008 0.786 ENST00000443562.1 0.008 0.846 ENST00000435692.2 0.009 0.846 ENST00000461448.1 0.010 0.179 ENST00000522312.1 0.010 0.197 ENST00000425776.1 0.010 0.872 ENST00000512349.1 0.010 0.162 ENST00000507698.1 0.010 0.816 ENST00000425896.1 0.010 0.769 ENST00000594976.1 0.011 0.299 ENST00000606468.1 0.011 0.812 ENST00000517595.1 0.011 0.205 ENST00000431130.2 0.011 0.821 ENST00000507627.1 0.011 0.812 ENST00000515842.1 0.012 0.179 ENST00000435880.2 0.012 0.197 ENST00000432267.2 0.012 0.812 ENST00000528818.1 0.012 0.205 ENST00000512417.1 0.012 0.812 ENST00000605147.1 0.012 0.171 ENST00000469289.1 0.013 0.855 ENST00000444721.1 0.013 0.812 ENST00000507653.1 0.013 0.179 ENST00000427042.1 0.013 0.829 ENST00000584829.1 0.013 0.803 ENST00000454595.1 0.013 0.821 ENST00000413525.1 0.013 0.218 ENST00000418050.1 0.014 0.821 ENST00000453569.1 0.014 0.222 ENST00000461864.1 0.014 0.162 ENST00000608056.1 0.015 0.171 ENST00000439745.1 0.016 0.226 ENST00000470739.1 0.016 0.197 ENST00000569694.1 0.016 0.162 ENST00000314957.3 0.016 0.752 ENST00000513304.1 0.016 0.179 ENST00000452176.1 0.034 0.786 ENST00000424748.1 0.016 0.803 ENST00000514201.1 0.016 0.769 ENST00000592948.1 0.017 0.214 ENST00000450500.1 0.017 0.795 ENST00000402410.2 0.017 0.821 ENST00000417926.1 0.017 0.778 ENST00000564407.1 0.017 0.222 ENST00000507476.1 0.017 0.821 ENST00000432711.1 0.018 0.795 ENST00000421563.1 0.018 0.812 ENST00000415342.1 0.019 0.222 ENST00000430471.1 0.019 0.786 ENST00000515263.1 0.019 0.205 ENST00000433475.1 0.019 0.872 ENST00000507056.1 0.019 0.248 ENST00000428647.1 0.019 0.786 ENST00000492307.1 0.020 0.803 ENST00000507781.1 0.020 0.291 ENST00000522173.1 0.020 0.205 ENST00000521803.1 0.020 0.795 ENST00000448129.1 0.021 0.197 ENST00000436293.2 0.021 0.855 ENST00000506425.1 0.021 0.214 ENST00000422841.1 0.021 0.222 ENST00000431244.1 0.022 0.222 ENST00000509057.1 0.022 0.786 ENST00000430520.1 0.023 0.222 ENST00000457686.1 0.023 0.282 ENST00000429315.3 0.023 0.744 ENST00000523895.1 0.024 0.222 ENST00000504728.1 0.024 0.752 ENST00000607148.1 0.025 0.214 ENST00000326734.1 0.025 0.248 ENST00000428624.1 0.025 0.222 ENST00000419531.2 0.025 0.214 ENST00000564261.1 0.026 0.769 ENST00000601854.1 0.026 0.735 ENST00000566904.1 0.026 0.812 ENST00000441036.1 0.026 0.812 ENST00000442036.1 0.026 0.786 ENST00000594101.1 0.026 0.239 ENST00000335577.4 0.026 0.786 ENST00000607594.1 0.027 0.778 ENST00000510165.1 0.027 0.214 ENST00000505149.1 0.027 0.282 ENST00000507681.1 0.027 0.222 ENST00000417636.1 0.027 0.795 ENST00000605082.1 0.028 0.752 ENST00000438623.1 0.028 0.222 ENST00000470263.1 0.028 0.778 ENST00000509641.2 0.029 0.752 ENST00000607804.1 0.029 0.786 ENST00000435492.1 0.030 0.226 ENST00000431139.2 0.030 0.769 ENST00000425275.1 0.030 0.214 ENST00000428176.1 0.030 0.265 ENST00000505109.1 0.031 0.769 ENST00000504207.1 0.031 0.231 ENST00000512401.1 0.031 0.226 ENST00000517916.1 0.031 0.752 ENST00000511213.1 0.031 0.778 ENST00000567486.2 0.031 0.761 ENST00000507842.1 0.032 0.769 ENST00000510648.1 0.032 0.786 ENST00000513851.1 0.032 0.752 ENST00000430677.1 0.032 0.256 ENST00000452283.1 0.032 0.726 ENST00000606314.1 0.033 0.803 ENST00000426702.1 0.033 0.256 ENST00000451396.2 0.033 0.735 ENST00000471248.1 0.034 0.239 ENST00000448379.1 0.034 0.735 ENST00000543656.1 0.034 0.761 ENST00000416080.1 0.034 0.752 ENST00000474250.1 0.034 0.744 ENST00000509105.1 0.034 0.744 ENST00000608740.1 0.035 0.769 ENST00000456327.1 0.035 0.744 ENST00000588145.1 0.035 0.803 ENST00000452901.1 0.035 0.786 ENST00000499583.1 0.036 0.248 ENST00000509559.1 0.036 0.256 ENST00000514608.1 0.036 0.214 ENST00000485020.1 0.037 0.291 ENST00000447876.1 0.037 0.282 ENST00000608851.1 0.037 0.265 ENST00000426892.1 0.037 0.752 ENST00000606200.1 0.037 0.752 ENST00000425176.1 0.037 0.295 ENST00000601136.1 0.037 0.829 ENST00000438978.1 0.038 0.761 ENST00000510254.1 0.038 0.214 ENST00000423410.1 0.038 0.752 ENST00000512603.1 0.039 0.265 ENST00000414120.1 0.040 0.282 ENST00000602528.1 0.040 0.265 ENST00000414625.2 0.040 0.239 ENST00000502410.1 0.040 0.778 ENST00000601940.1 0.041 0.239 ENST00000505162.1 0.041 0.744 ENST00000492209.1 0.041 0.786 ENST00000427748.1 0.042 0.239 ENST00000522975.1 0.042 0.726 ENST00000606855.1 0.042 0.744 ENST00000508031.1 0.043 0.744 ENST00000609032.1 0.043 0.231 ENST00000446073.1 0.043 0.761 ENST00000424084.1 0.044 0.778 ENST00000507639.1 0.044 0.718 ENST00000413531.1 0.044 0.274 ENST00000434346.1 0.044 0.299 ENST00000417516.1 0.044 0.803 ENST00000416279.1 0.044 0.795 ENST00000443270.1 0.044 0.795 ENST00000436262.1 0.045 0.222 ENST00000503179.1 0.046 0.231 ENST00000510240.1 0.046 0.256 ENST00000607744.1 0.046 0.231 ENST00000512428.1 0.046 0.274 ENST00000511390.1 0.046 0.774 ENST00000456519.1 0.046 0.274 ENST00000506950.1 0.047 0.265 ENST00000598740.1 0.047 0.744 ENST00000520041.1 0.047 0.752 ENST00000417927.1 0.047 0.282 ENST00000523311.1 0.047 0.756 ENST00000432395.1 0.047 0.214 ENST00000502467.1 0.047 0.248 ENST00000609166.1 0.047 0.744 ENST00000609005.1 0.047 0.761 ENST00000444042.2 0.047 0.795 ENST00000511616.1 0.048 0.282 ENST00000426539.1 0.048 0.299 ENST00000412204.2 0.048 0.735 ENST00000436950.1 0.048 0.761 ENST00000496220.1 0.048 0.726 ENST00000569928.1 0.049 0.239 ENST00000433108.1 0.049 0.752 ENST00000507398.1 0.049 0.274 ENST00000414199.1 0.049 0.769

The lncRNAs listed can be used as biomarkers for the prediction of Left Ventricular Remodeling and as therapeutics targets to prevent development of Heart Failure. 

1. A Method of diagnosing or monitoring or treating primary and secondary cardiac diseases or disorders in a subject, the method comprising a.) obtaining a sample from said subject; b.) detecting the level of expression of one or more lncRNAs (e.g., having a sequence selected from the group consisting of SEQ ID NO1 to SEQ ID NO 3238, isoforms thereof, fragment thereof and variant sharing at least 80% nucleotide sequence homology); and c.) diagnosing the subject with one or more cardiac diseases or disorders based upon the level of expression of one or more lncRNAs compared to a control, with the proviso that the one or more lncRNAs are not selected from the group consisting of lncRNAs of Table 1, fragments thereof, isoforms thereof and variants sharing at least 80% nucleotide sequence identity thereto.
 2. The method of claim 1, wherein the level of expression of one or more said lncRNAs indicates that the subject has developed or is at risk of developing a cardiac disorder.
 3. The method of claim 1, wherein cardiac disorder is selected from the group consisting of: pathologies or abnormalities with Interventricular Septal Thickness (IVS), heart failures (e.g., left and right ventricle dilatation/dysfunction), EF, LVID, MI, HFrEF, HFpEF, myocardial infarction, myocarditis (e.g., viral myocarditis), cardiac toxicity, brachycardia, arrhythmia, congenital heart defects, hypertension, diabetic cardiomyopathy, idiopathic and dilated cardiomyopathy, pathologies characterized by malformation, pathologies characterized by tissue remodeling, pathologies characterized by affected function, pathologies characterized by disorders of the right heart, pathologies characterized by arrhythmias, pathologies characterized by intoxication, pathologies characterized by cancer, pathologies characterized by neurologic disorders, pathologies characterized by trauma, pathologies characterized by a change in hemodynamic, pathologies characterized by vascular disorders altering cardiac functions such as Coronary artery disease (CAD), and pathologies resulted from cardiac dysfunction/disorders inducing ischemic (embolic/thrombotic) stroke.
 4. The method claim 1, wherein the diagnosis step includes predicting the development of heart failure in a subject having suffered AMI, and wherein the level of expression of one or more said lncRNAs predicts the risk for the subject to develop HF.
 5. The method of claim 1, wherein the method further comprises the step of administering at least one pharmaceutical to the subject in order to treat one or more cardiovascular diseases or disorders.
 6. The method of claim 1, wherein the biological sample is selected from the group consisting of: whole blood, serum, plasma, semen, saliva, tears, urine, fecal material, sweat, buccal smears, skin, cardiac tissue, liver, brain tissue, amniotic fluid, nerve tissue and hair (e.g, wherein the sample is preferably plasma or cardiac tissue).
 7. The method of claim 1, wherein the lncRNA expression levels are detected in a sample (e.g., biological sample) using a technique selected from the group consisting of: Si nuclease protection assay, microarray analysis, polymerase chain reaction (PCR), hybridization technologies, reverse transcriptase polymerase chain reaction (RT-PCR), Northern blot, serial analysis of gene expression (SAGE), immunoassay, and mass spectrometry.
 8. The method of claim 1, wherein the lncRNA expression level of lncRNA in sample (e.g., biological sample) is detected using a singleplexed or multiplexed method selected from a group consisting of: fluorescence, luminescence, radio-marking, next generation sequencing and/or coded microdisks.
 9. The method of claim 1, wherein the expression level of the lncRNAs of the invention are detected by measuring the levels of cDNAs, amplified RNAs or DNAs or quantities of DNA probes, or other molecules, in a sample (e.g., biological sample) that are indicative of the expression level of the lncRNA.
 10. The method of claim 1, wherein the lncRNA which is detected is selected from any of SEQ ID NO: 1-SEQ ID NO:
 3238. 11. The method of claim 10, wherein the lncRNA which is detected is selected from the group consisting of: (i) 15 lncRNAs of SEQ ID 1204, SEQ ID 1736, SEQ ID 0544, SEQ ID 0915, SEQ ID2368, SEQ ID 1595, SEQ ID 2382, SEQ ID 0859, SEQ ID 3112, SEQ ID 1869, SEQ ID 1406, SEQ ID 0043, SEQ ID 0363, SEQ ID 0069 and SEQ ID 1947; (ii) 11 lncRNAs of SEQ ID 2373, SEQ ID 1748, SEQ ID 3112, SEQ ID 1231, SEQ ID 0664, SEQ ID 1686, SEQ ID 0791, SEQ ID 2126, SEQ ID 2750, SEQ ID 3010, and SEQ ID 2241; (iii) 14 lncRNAs of SEQ ID 2150, SEQ ID 1534, SEQ ID 0311, SEQ ID 2952, SEQ ID 2838, SEQ ID 1437, SEQ ID 1297, SEQ ID 1059, SEQ ID 1465, SEQ ID 2826, SEQ ID 0180, SEQ ID 0538, SEQ ID 0258, and SEQ ID 2273; (iv) 20 lncRNAs of SEQ ID 0190, SEQ ID 0359, SEQ ID 0776, SEQ ID 1421, SEQ ID 1795, SEQ ID 0477, SEQ ID 1511, SEQ ID 0435, SEQ ID 1418, SEQ ID 1025, SEQ ID 0265, SEQ ID 1311, SEQ ID 2540, SEQ ID 2323, SEQ ID 3011, SEQ ID 2447, SEQ ID 2863, SEQ ID 2697, SEQ ID 3128, and SEQ ID 2265; (v) 11 lncRNAs of SEQ ID 2540, SEQ ID 0545, SEQ ID 1766, SEQ ID 3011, SEQ ID 0968, SEQ ID 2371, SEQ ID 1533, SEQ ID 0749, SEQ ID 0609, SEQ ID 1446, and SEQ ID 2986; (vi) 8 lncRNAs of SEQ1204, SEQ2454, SEQ0334, SEQ1403, SEQ1089, SEQ2692, SEQ2273, SEQ0502; (vii) 4 lncRNAs of SEQ0097, SEQ1947, SEQ1051 and SEQ2996; and (viii) lncRNAs in Table 4, Table 5, Table 8, Table 9, Table 12, Table 15, Table 18, Table 19, Table 20, Table 21, Table 22, Table 24, Table 25, Table 28, Table 29, Table 32, Table 33, Table 34, Table 35, Table 36, Table 37, Table 38, Table 39, Table 40, and/or Table
 41. 12. A method for monitoring treatment efficacy in a subject suffering from a primary and secondary cardiac disease or disorder and receiving a pharmaceutical cardiac therapy, the method comprising a.) administering a pharmaceutical to a subject suffering from cardiac injury; b.) obtaining a sample (e.g., a biological sample) from the subject; c.) detecting the level of expression of one or more lncRNAs (e.g., having a sequence selected from the group consisting of SEQ ID NO1 to SEQ ID NO 3238, isoforms thereof, fragment thereof and variant sharing at least 80% nucleotide sequence homology) in the sample, wherein the expression level of lncRNA is compared to a control; and d.) determining the level of expression of one or more lncRNAs, wherein the level of expression of said one or more lncRNAs indicates the efficacy, non-efficacy or toxicity of the treatment, with the proviso that the one or more lncRNAs are not selected from the group consisting of lncRNAs of Table 1, fragments thereof, isoforms thereof and variants sharing at least 80% nucleotide sequence identity thereto.
 13. A method for diagnosing drug-induced cardiac toxicity in a subject receiving a pharmaceutical composition, wherein the method comprises a.) obtaining a sample from the subject; b.) measuring the level of expression, (e.g., in a biological sample derived from said subject) of one or more lncRNAs of the invention from the sample c.) diagnosing the subject as having a cardiac toxicity from the pharmaceutical composition depending upon the level of expression of one or more said lncRNAs, with the proviso that the one or more lncRNAs are not selected from the group consisting of lncRNAs of Table 1, fragments thereof, isoforms thereof and variants sharing at least 80% nucleotide sequence identity thereto.
 14. (canceled)
 15. (canceled)
 16. (canceled)
 17. (canceled)
 18. (canceled)
 19. (canceled)
 20. A diagnostic/prognostic/disease activity/theranostic kit for carrying out the method of claim
 1. 21. The kit of claim 20, wherein the kit comprises: (i) one or more oligonucleotide probes comprising a sequence complementary to a region of one or more lncRNAs selected from the group consisting of SEQ ID NO 1 to SEQ ID NO 3238, isoforms thereof, fragment thereof and variant sharing at least 80% nucleotide sequence homology and (ii) a reagent for purifying the probe-target nucleic acid complexes.
 22. The kit of claim 21, wherein the oligonucleotide probes are biotinylated and the reagent for purifying the probe-target complexes is a streptavidin-coated substrate, e.g, a streptavidin-coated magnetic particle.
 23. The kit of claim 21, wherein the one or more lncRNAs are selected from the group consisting of: (i) 15 lncRNAs of SEQ ID 1204, SEQ ID 1736, SEQ ID 0544, SEQ ID 0915, SEQ ID2368, SEQ ID 1595, SEQ ID 2382, SEQ ID 0859, SEQ ID 3112, SEQ ID 1869, SEQ ID 1406, SEQ ID 0043, SEQ ID 0363, SEQ ID 0069 and SEQ ID 1947; (ii) 11 lncRNAs of SEQ ID 2373, SEQ ID 1748, SEQ ID 3112, SEQ ID 1231, SEQ ID 0664, SEQ ID 1686, SEQ ID 0791, SEQ ID 2126, SEQ ID 2750, SEQ ID 3010, and SEQ ID 2241; (iii) 14 lncRNAs of SEQ ID 2150, SEQ ID 1534, SEQ ID 0311, SEQ ID 2952, SEQ ID 2838, SEQ ID 1437, SEQ ID 1297, SEQ ID 1059, SEQ ID 1465, SEQ ID 2826, SEQ ID 0180, SEQ ID 0538, SEQ ID 0258, and SEQ ID 2273; (iv) 20 lncRNAs of SEQ ID 0190, SEQ ID 0359, SEQ ID 0776, SEQ ID 1421, SEQ ID 1795, SEQ ID 0477, SEQ ID 1511, SEQ ID 0435, SEQ ID 1418, SEQ ID 1025, SEQ ID 0265, SEQ ID 1311, SEQ ID 2540, SEQ ID 2323, SEQ ID 3011, SEQ ID 2447, SEQ ID 2863, SEQ ID 2697, SEQ ID 3128, and SEQ ID 2265; (v) 11 lncRNAs of SEQ ID 2540, SEQ ID 0545, SEQ ID 1766, SEQ ID 3011, SEQ ID 0968, SEQ ID 2371, SEQ ID 1533, SEQ ID 0749, SEQ ID 0609, SEQ ID 1446, and SEQ ID 2986; (vi) 8 lncRNAs of SEQ1204, SEQ2454, SEQ0334, SEQ1403, SEQ1089, SEQ2692, SEQ2273, SEQ0502; (vii) 4 lncRNAs of SEQ0097, SEQ1947, SEQ1051 and SEQ2996; and (viii) lncRNAs in Table 4, Table 5, Table 8, Table 9, Table 12, Table 15, Table 18, Table 19, Table 20, Table 21, Table 22, Table 24, Table 25, Table 28, Table 29, Table 32, Table 33, Table 34, Table 35, Table 36, Table 37, Table 38, Table 39, Table 40, and/or Table
 41. 